8GBT | pdb_00008gbt

Time-resolve SFX structure of a photoproduct of carbon monoxide complex of bovine cytochrome c oxidase

PDB DOI: https://doi.org/10.2210/pdb8GBT/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Bos taurus
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2023-02-28 Released: 2023-09-20
Deposition Author(s): Ishigami, I., Yeh, S.-R., Rousseau, D.L.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.269 (Depositor), 0.287 (DCC)
R-Value Work:
0.223 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Detection of a Geminate Photoproduct of Bovine Cytochrome c Oxidase by Time-Resolved Serial Femtosecond Crystallography.

Ishigami, I., Carbajo, S., Zatsepin, N., Hikita, M., Conrad, C.E., Nelson, G., Coe, J., Basu, S., Grant, T., Seaberg, M.H., Sierra, R.G., Hunter, M.S., Fromme, P., Fromme, R., Rousseau, D.L., Yeh, S.R.

(2023) J Am Chem Soc 145: 22305-22309

PubMed: 37695261 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/jacs.3c07803
Primary Citation Related Structures:
8GBT

PubMed Abstract:
Cytochrome c oxidase (C c O) is a large membrane-bound hemeprotein that catalyzes the reduction of dioxygen to water. Unlike classical dioxygen binding hemeproteins with a heme b group in their active sites, C c O has a unique binuclear center (BNC) composed of a copper atom (Cu _B) and a heme a ₃ iron, where O ₂ binds and is reduced to water. CO is a versatile O ₂ surrogate in ligand binding and escape reactions. Previous time-resolved spectroscopic studies of the CO complexes of bovine C c O (bC c O) revealed that photolyzing CO from the heme a ₃ iron leads to a metastable intermediate (Cu _B-CO), where CO is bound to Cu _B, before it escapes out of the BNC. Here, with a pump-probe based time-resolved serial femtosecond X-ray crystallography, we detected a geminate photoproduct of the bC c O-CO complex, where CO is dissociated from the heme a ₃ iron and moved to a temporary binding site midway between the Cu _B and the heme a ₃ iron, while the locations of the two metal centers and the conformation of Helix-X, housing the proximal histidine ligand of the heme a ₃ iron, remain in the CO complex state. This new structure, combined with other reported structures of bC c O, allows for a clearer definition of the ligand dissociation trajectory as well as the associated protein dynamics.

Organizational Affiliation

Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, United States.

Macromolecule Content

Total Structure Weight: 443.14 kDa
Atom Count: 30,981
Modeled Residue Count: 3,556
Deposited Residue Count: 3,614
Unique protein chains: 13

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 1	A, N	514	Bos taurus	Mutation(s): 0 EC: 1.9.3.1 (PDB Primary Data), 7.1.1.9 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P00396 (Bos taurus) Explore P00396 Go to UniProtKB: P00396
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00396
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 2	B, O	227	Bos taurus	Mutation(s): 0 EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for P68530 (Bos taurus) Explore P68530 Go to UniProtKB: P68530
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68530
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 3	C, P	261	Bos taurus	Mutation(s): 0 EC: 7.1.1.9 Membrane Entity: Yes
UniProt
Find proteins for P00415 (Bos taurus) Explore P00415 Go to UniProtKB: P00415
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00415
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Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 4 isoform 1, mitochondrial	D, Q	147	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00423 (Bos taurus) Explore P00423 Go to UniProtKB: P00423
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00423
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 5A, mitochondrial	E, R	109	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00426 (Bos taurus) Explore P00426 Go to UniProtKB: P00426
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00426
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Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 5B, mitochondrial	F, S	98	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00428 (Bos taurus) Explore P00428 Go to UniProtKB: P00428
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00428
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Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6A2, mitochondrial	G, T	85	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P07471 (Bos taurus) Explore P07471 Go to UniProtKB: P07471
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07471
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6B1	H, U	85	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00429 (Bos taurus) Explore P00429 Go to UniProtKB: P00429
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00429
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 6C	I, V	73	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P04038 (Bos taurus) Explore P04038 Go to UniProtKB: P04038
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04038
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Reference Sequence

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| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7A1, mitochondrial	J, W	59	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P07470 (Bos taurus) Explore P07470 Go to UniProtKB: P07470
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07470
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Reference Sequence

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| 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7B, mitochondrial	K, X	56	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P13183 (Bos taurus) Explore P13183 Go to UniProtKB: P13183
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13183
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Reference Sequence

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| 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 7C, mitochondrial	L, Y	47	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P00430 (Bos taurus) Explore P00430 Go to UniProtKB: P00430
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00430
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome c oxidase subunit 8B, mitochondrial	M, Z	46	Bos taurus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P10175 (Bos taurus) Explore P10175 Go to UniProtKB: P10175
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10175
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Reference Sequence

Small Molecules

Ligands 16 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download:Ideal Coordinates CCD File SDF format, chain VA [auth G] SDF format, chain TB [auth P] SDF format, chain OA [auth C] SDF format, chain BC [auth T] MOL2 format, chain VA [auth G] MOL2 format, chain TB [auth P] MOL2 format, chain OA [auth C] MOL2 format, chain BC [auth T] mmCIF format, chain VA [auth G] mmCIF format, chain TB [auth P] mmCIF format, chain OA [auth C] mmCIF format, chain BC [auth T]	BC [auth T], OA [auth C], TB [auth P], VA [auth G]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain BC [auth T] Focus chain OA [auth C] Focus chain TB [auth P] Focus chain VA [auth G]
TGL Query on TGL Download:Ideal Coordinates CCD File SDF format, chain YA [auth I] SDF format, chain LB [auth N] SDF format, chain JB [auth N] SDF format, chain FA [auth A] SDF format, chain EC [auth Y] SDF format, chain BB [auth L] MOL2 format, chain YA [auth I] MOL2 format, chain LB [auth N] MOL2 format, chain JB [auth N] MOL2 format, chain FA [auth A] MOL2 format, chain EC [auth Y] MOL2 format, chain BB [auth L] mmCIF format, chain YA [auth I] mmCIF format, chain LB [auth N] mmCIF format, chain JB [auth N] mmCIF format, chain FA [auth A] mmCIF format, chain EC [auth Y] mmCIF format, chain BB [auth L]	BB [auth L] EC [auth Y] FA [auth A] JB [auth N] LB [auth N] BB [auth L], EC [auth Y], FA [auth A], JB [auth N], LB [auth N], YA [auth I]	TRISTEAROYLGLYCEROL C₅₇ H₁₁₀ O₆ DCXXMTOCNZCJGO-UHFFFAOYSA-N		Interactions Focus chain BB [auth L] Focus chain EC [auth Y] Focus chain FA [auth A] Focus chain JB [auth N] Focus chain LB [auth N] Focus chain YA [auth I]
HEA (Subject of Investigation/LOI) Query on HEA Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain FB [auth N] SDF format, chain EB [auth N] SDF format, chain BA [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain FB [auth N] MOL2 format, chain EB [auth N] MOL2 format, chain BA [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain FB [auth N] mmCIF format, chain EB [auth N] mmCIF format, chain BA [auth A]	AA [auth A], BA [auth A], EB [auth N], FB [auth N]	HEME-A C₄₉ H₅₆ Fe N₄ O₆ ZGGYGTCPXNDTRV-PRYGPKJJSA-L		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain EB [auth N] Focus chain FB [auth N]
PEK Query on PEK Download:Ideal Coordinates CCD File SDF format, chain YB [auth T] SDF format, chain XA [auth G] SDF format, chain UA [auth G] SDF format, chain SA [auth G] SDF format, chain RB [auth P] SDF format, chain AC [auth T] MOL2 format, chain YB [auth T] MOL2 format, chain XA [auth G] MOL2 format, chain UA [auth G] MOL2 format, chain SA [auth G] MOL2 format, chain RB [auth P] MOL2 format, chain AC [auth T] mmCIF format, chain YB [auth T] mmCIF format, chain XA [auth G] mmCIF format, chain UA [auth G] mmCIF format, chain SA [auth G] mmCIF format, chain RB [auth P] mmCIF format, chain AC [auth T]	AC [auth T] RB [auth P] SA [auth G] UA [auth G] XA [auth G] AC [auth T], RB [auth P], SA [auth G], UA [auth G], XA [auth G], YB [auth T]	(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL (5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE C₄₃ H₇₈ N O₈ P ANRKEHNWXKCXDB-BHFWLYLHSA-N		Interactions Focus chain AC [auth T] Focus chain RB [auth P] Focus chain SA [auth G] Focus chain UA [auth G] Focus chain XA [auth G] Focus chain YB [auth T]
PSC (Subject of Investigation/LOI) Query on PSC Download:Ideal Coordinates CCD File SDF format, chain QA [auth E] SDF format, chain WB [auth R] MOL2 format, chain QA [auth E] MOL2 format, chain WB [auth R] mmCIF format, chain QA [auth E] mmCIF format, chain WB [auth R]	QA [auth E], WB [auth R]	(7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM 4-OXIDE C₄₂ H₈₁ N O₈ P JLPULHDHAOZNQI-AUSZDXHESA-O		Interactions Focus chain QA [auth E] Focus chain WB [auth R]
PGV (Subject of Investigation/LOI) Query on PGV Download:Ideal Coordinates CCD File SDF format, chain SB [auth P] SDF format, chain NA [auth C] SDF format, chain MA [auth C] SDF format, chain KB [auth N] SDF format, chain GA [auth A] SDF format, chain FC [auth Z] SDF format, chain CC [auth U] SDF format, chain CB [auth M] MOL2 format, chain SB [auth P] MOL2 format, chain NA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain KB [auth N] MOL2 format, chain GA [auth A] MOL2 format, chain FC [auth Z] MOL2 format, chain CC [auth U] MOL2 format, chain CB [auth M] mmCIF format, chain SB [auth P] mmCIF format, chain NA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain KB [auth N] mmCIF format, chain GA [auth A] mmCIF format, chain FC [auth Z] mmCIF format, chain CC [auth U] mmCIF format, chain CB [auth M]	CB [auth M] CC [auth U] FC [auth Z] GA [auth A] KB [auth N] CB [auth M], CC [auth U], FC [auth Z], GA [auth A], KB [auth N], MA [auth C], NA [auth C], SB [auth P]	(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE C₄₀ H₇₇ O₁₀ P ADYWCMPUNIVOEA-GPJPVTGXSA-N		Interactions Focus chain CB [auth M] Focus chain CC [auth U] Focus chain FC [auth Z] Focus chain GA [auth A] Focus chain KB [auth N] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain SB [auth P]
DMU (Subject of Investigation/LOI) Query on DMU Download:Ideal Coordinates CCD File SDF format, chain ZB [auth T] SDF format, chain VB [auth Q] SDF format, chain TA [auth G] SDF format, chain DB [auth M] MOL2 format, chain ZB [auth T] MOL2 format, chain VB [auth Q] MOL2 format, chain TA [auth G] MOL2 format, chain DB [auth M] mmCIF format, chain ZB [auth T] mmCIF format, chain VB [auth Q] mmCIF format, chain TA [auth G] mmCIF format, chain DB [auth M]	DB [auth M], TA [auth G], VB [auth Q], ZB [auth T]	DECYL-BETA-D-MALTOPYRANOSIDE C₂₂ H₄₂ O₁₁ WOQQAWHSKSSAGF-WXFJLFHKSA-N		Interactions Focus chain DB [auth M] Focus chain TA [auth G] Focus chain VB [auth Q] Focus chain ZB [auth T]
CHD Query on CHD Download:Ideal Coordinates CCD File SDF format, chain WA [auth G] SDF format, chain UB [auth P] SDF format, chain QB [auth P] SDF format, chain PA [auth C] SDF format, chain MB [auth N] SDF format, chain KA [auth C] SDF format, chain JA [auth B] SDF format, chain AB [auth J] MOL2 format, chain WA [auth G] MOL2 format, chain UB [auth P] MOL2 format, chain QB [auth P] MOL2 format, chain PA [auth C] MOL2 format, chain MB [auth N] MOL2 format, chain KA [auth C] MOL2 format, chain JA [auth B] MOL2 format, chain AB [auth J] mmCIF format, chain WA [auth G] mmCIF format, chain UB [auth P] mmCIF format, chain QB [auth P] mmCIF format, chain PA [auth C] mmCIF format, chain MB [auth N] mmCIF format, chain KA [auth C] mmCIF format, chain JA [auth B] mmCIF format, chain AB [auth J]	AB [auth J] JA [auth B] KA [auth C] MB [auth N] PA [auth C] AB [auth J], JA [auth B], KA [auth C], MB [auth N], PA [auth C], QB [auth P], UB [auth P], WA [auth G]	CHOLIC ACID C₂₄ H₄₀ O₅ BHQCQFFYRZLCQQ-OELDTZBJSA-N		Interactions Focus chain AB [auth J] Focus chain JA [auth B] Focus chain KA [auth C] Focus chain MB [auth N] Focus chain PA [auth C] Focus chain QB [auth P] Focus chain UB [auth P] Focus chain WA [auth G]
SAC (Subject of Investigation/LOI) Query on SAC Download:Ideal Coordinates CCD File SDF format, chain DC [auth V] SDF format, chain ZA [auth I] MOL2 format, chain DC [auth V] MOL2 format, chain ZA [auth I] mmCIF format, chain DC [auth V] mmCIF format, chain ZA [auth I]	DC [auth V], ZA [auth I]	N-ACETYL-SERINE C₅ H₉ N O₄ JJIHLJJYMXLCOY-BYPYZUCNSA-N		Interactions Focus chain DC [auth V] Focus chain ZA [auth I]
CUA Query on CUA Download:Ideal Coordinates CCD File SDF format, chain OB [auth O] SDF format, chain IA [auth B] MOL2 format, chain OB [auth O] MOL2 format, chain IA [auth B] mmCIF format, chain OB [auth O] mmCIF format, chain IA [auth B]	IA [auth B], OB [auth O]	DINUCLEAR COPPER ION Cu₂ ALKZAGKDWUSJED-UHFFFAOYSA-N		Interactions Focus chain IA [auth B] Focus chain OB [auth O]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain XB [auth S] SDF format, chain RA [auth F] MOL2 format, chain XB [auth S] MOL2 format, chain RA [auth F] mmCIF format, chain XB [auth S] mmCIF format, chain RA [auth F]	RA [auth F], XB [auth S]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain RA [auth F] Focus chain XB [auth S]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain GB [auth N] SDF format, chain CA [auth A] MOL2 format, chain GB [auth N] MOL2 format, chain CA [auth A] mmCIF format, chain GB [auth N] mmCIF format, chain CA [auth A]	CA [auth A], GB [auth N]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Focus chain GB [auth N]
CMO Query on CMO Download:Ideal Coordinates CCD File SDF format, chain NB [auth N] SDF format, chain HA [auth A] MOL2 format, chain NB [auth N] MOL2 format, chain HA [auth A] mmCIF format, chain NB [auth N] mmCIF format, chain HA [auth A]	HA [auth A], NB [auth N]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N		Interactions Focus chain HA [auth A] Focus chain NB [auth N]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain HB [auth N] SDF format, chain DA [auth A] MOL2 format, chain HB [auth N] MOL2 format, chain DA [auth A] mmCIF format, chain HB [auth N] mmCIF format, chain DA [auth A]	DA [auth A], HB [auth N]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DA [auth A] Focus chain HB [auth N]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain IB [auth N] SDF format, chain EA [auth A] MOL2 format, chain IB [auth N] MOL2 format, chain EA [auth A] mmCIF format, chain IB [auth N] mmCIF format, chain EA [auth A]	EA [auth A], IB [auth N]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain EA [auth A] Focus chain IB [auth N]
OH Query on OH Download:Ideal Coordinates CCD File SDF format, chain PB [auth P] SDF format, chain LA [auth C] MOL2 format, chain PB [auth P] MOL2 format, chain LA [auth C] mmCIF format, chain PB [auth P] mmCIF format, chain LA [auth C]	LA [auth C], PB [auth P]	HYDROXIDE ION H O XLYOFNOQVPJJNP-UHFFFAOYSA-M		Interactions Focus chain LA [auth C] Focus chain PB [auth P]

Modified Residues 3 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME Query on FME	A, N	L-PEPTIDE LINKING	C₆ H₁₁ N O₃ S		MET
TPO Query on TPO	G, T	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR
SAC Query on SAC	I, V	L-PEPTIDE LINKING	C₅ H₉ N O₄		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.269 (Depositor), 0.287 (DCC)
R-Value Work: 0.223 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 178.3	α = 90
b = 189	β = 90
c = 209	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystFEL	data reduction
CrystFEL	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-09-20

Deposition Author(s):

Ishigami, I.

Yeh, S.-R.

Rousseau, D.L.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM115773-01A1
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5R01GM115773-02
National Science Foundation (NSF, United States)	United States	1404929

Revision History (Full details and data files)

Version 1.0: 2023-09-20
Type: Initial release
Version 1.1: 2023-09-27
Changes: Database references
Version 1.2: 2023-11-01
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

8GBT | pdb_00008gbt

Time-resolve SFX structure of a photoproduct of carbon monoxide complex of bovine cytochrome c oxidase

Literature

Detection of a Geminate Photoproduct of Bovine Cytochrome c Oxidase by Time-Resolved Serial Femtosecond Crystallography.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)