3WG7 | pdb_00003wg7

A 1.9 angstrom radiation damage free X-ray structure of large (420KDa) protein by femtosecond crystallography

PDB DOI: https://doi.org/10.2210/pdb3WG7/pdb

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

Deposited: 2013-07-29 Released: 2014-04-30
Deposition Author(s): Hirata, K., Shinzawa-Itoh, K., Yano, N., Takemura, S., Kato, K., Hatanaka, M., Muramoto, K., Kawahara, T., Tsukihara, T., Yamashita, E., Tono, K., Ueno, G., Hikima, T., Murakami, H., Inubushi, Y., Yabashi, M., Ishikawa, T., Yamamoto, M., Ogura, T., Sugimoto, H., Shen, J.R., Yoshikawa, S., Ago, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.230 (Depositor), 0.248 (DCC)
R-Value Work:
0.195 (Depositor), 0.218 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL.

Hirata, K., Shinzawa-Itoh, K., Yano, N., Takemura, S., Kato, K., Hatanaka, M., Muramoto, K., Kawahara, T., Tsukihara, T., Yamashita, E., Tono, K., Ueno, G., Hikima, T., Murakami, H., Inubushi, Y., Yabashi, M., Ishikawa, T., Yamamoto, M., Ogura, T., Sugimoto, H., Shen, J.R., Yoshikawa, S., Ago, H.

(2014) Nat Methods 11: 734-736

PubMed: 24813624 Search on PubMed
DOI: https://doi.org/10.1038/nmeth.2962
Primary Citation Related Structures:
3WG7, 7Y44

PubMed Abstract:
We report a method of femtosecond crystallography for solving radiation damage-free crystal structures of large proteins at sub-angstrom spatial resolution, using a large single crystal and the femtosecond pulses of an X-ray free-electron laser (XFEL). We demonstrated the performance of the method by determining a 1.9-Å radiation damage-free structure of bovine cytochrome c oxidase, a large (420-kDa), highly radiation-sensitive membrane protein.

Organizational Affiliation

1] RIKEN SPring-8 Center, Sayo, Japan. [2] Japan Science and Technology Agency (JST), Core Research for Evolutional Science and Technology (CREST), Kawaguchi, Japan. [3].

Macromolecule Content

Total Structure Weight: 441.9 kDa
Atom Count: 33,302
Modeled Residue Count: 3,558
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
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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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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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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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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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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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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
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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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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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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
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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 14 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download:Ideal Coordinates CCD File SDF format, chain PA [auth C] SDF format, chain RB [auth P] SDF format, chain WA [auth G] SDF format, chain YB [auth T] MOL2 format, chain PA [auth C] MOL2 format, chain RB [auth P] MOL2 format, chain WA [auth G] MOL2 format, chain YB [auth T] mmCIF format, chain PA [auth C] mmCIF format, chain RB [auth P] mmCIF format, chain WA [auth G] mmCIF format, chain YB [auth T]	PA [auth C], RB [auth P], WA [auth G], YB [auth T]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain PA [auth C] Focus chain RB [auth P] Focus chain WA [auth G] Focus chain YB [auth T] Interactions & Density Focus chain PA [auth C] Focus chain RB [auth P] Focus chain WA [auth G] Focus chain YB [auth T]
TGL Query on TGL Download:Ideal Coordinates CCD File SDF format, chain AB [auth L] SDF format, chain AC [auth Y] SDF format, chain IA [auth B] SDF format, chain UA [auth D] SDF format, chain VB [auth Q] SDF format, chain KB [auth N] MOL2 format, chain AB [auth L] MOL2 format, chain AC [auth Y] MOL2 format, chain IA [auth B] MOL2 format, chain UA [auth D] MOL2 format, chain VB [auth Q] MOL2 format, chain KB [auth N] mmCIF format, chain AB [auth L] mmCIF format, chain AC [auth Y] mmCIF format, chain IA [auth B] mmCIF format, chain UA [auth D] mmCIF format, chain VB [auth Q] mmCIF format, chain KB [auth N]	AB [auth L] AC [auth Y] IA [auth B] KB [auth N] UA [auth D] AB [auth L], AC [auth Y], IA [auth B], KB [auth N], UA [auth D], VB [auth Q]	TRISTEAROYLGLYCEROL C₅₇ H₁₁₀ O₆ DCXXMTOCNZCJGO-UHFFFAOYSA-N		Interactions Focus chain AB [auth L] Focus chain AC [auth Y] Focus chain IA [auth B] Focus chain KB [auth N] Focus chain UA [auth D] Focus chain VB [auth Q] Interactions & Density Focus chain AB [auth L] Focus chain AC [auth Y] Focus chain IA [auth B] Focus chain KB [auth N] Focus chain UA [auth D] Focus chain VB [auth Q]
HEA Query on HEA Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain CB [auth N] SDF format, chain DB [auth N] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain CB [auth N] MOL2 format, chain DB [auth N] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain CB [auth N] mmCIF format, chain DB [auth N]	AA [auth A], BA [auth A], CB [auth N], DB [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 CB [auth N] Focus chain DB [auth N] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CB [auth N] Focus chain DB [auth N]
PEK Query on PEK Download:Ideal Coordinates CCD File SDF format, chain NA [auth C] SDF format, chain PB [auth P] SDF format, chain SA [auth C] SDF format, chain UB [auth P] SDF format, chain XB [auth T] SDF format, chain XA [auth G] MOL2 format, chain NA [auth C] MOL2 format, chain PB [auth P] MOL2 format, chain SA [auth C] MOL2 format, chain UB [auth P] MOL2 format, chain XB [auth T] MOL2 format, chain XA [auth G] mmCIF format, chain NA [auth C] mmCIF format, chain PB [auth P] mmCIF format, chain SA [auth C] mmCIF format, chain UB [auth P] mmCIF format, chain XB [auth T] mmCIF format, chain XA [auth G]	NA [auth C] PB [auth P] SA [auth C] UB [auth P] XA [auth G] NA [auth C], PB [auth P], SA [auth C], UB [auth P], XA [auth G], XB [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 NA [auth C] Focus chain PB [auth P] Focus chain SA [auth C] Focus chain UB [auth P] Focus chain XA [auth G] Focus chain XB [auth T] Interactions & Density Focus chain NA [auth C] Focus chain PB [auth P] Focus chain SA [auth C] Focus chain UB [auth P] Focus chain XA [auth G] Focus chain XB [auth T]
PSC Query on PSC Download:Ideal Coordinates CCD File SDF format, chain LA [auth B] SDF format, chain LB [auth N] MOL2 format, chain LA [auth B] MOL2 format, chain LB [auth N] mmCIF format, chain LA [auth B] mmCIF format, chain LB [auth N]	LA [auth B], LB [auth N]	(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 LA [auth B] Focus chain LB [auth N] Interactions & Density Focus chain LA [auth B] Focus chain LB [auth N]
PGV Query on PGV Download:Ideal Coordinates CCD File SDF format, chain GA [auth A] SDF format, chain IB [auth N] SDF format, chain NB [auth P] SDF format, chain QB [auth P] SDF format, chain TA [auth C] SDF format, chain OA [auth C] SDF format, chain JB [auth N] SDF format, chain HA [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain IB [auth N] MOL2 format, chain NB [auth P] MOL2 format, chain QB [auth P] MOL2 format, chain TA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain JB [auth N] MOL2 format, chain HA [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain IB [auth N] mmCIF format, chain NB [auth P] mmCIF format, chain QB [auth P] mmCIF format, chain TA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain JB [auth N] mmCIF format, chain HA [auth A]	GA [auth A] HA [auth A] IB [auth N] JB [auth N] NB [auth P] GA [auth A], HA [auth A], IB [auth N], JB [auth N], NB [auth P], OA [auth C], QB [auth P], TA [auth C]	(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 GA [auth A] Focus chain HA [auth A] Focus chain IB [auth N] Focus chain JB [auth N] Focus chain NB [auth P] Focus chain OA [auth C] Focus chain QB [auth P] Focus chain TA [auth C] Interactions & Density Focus chain GA [auth A] Focus chain HA [auth A] Focus chain IB [auth N] Focus chain JB [auth N] Focus chain NB [auth P] Focus chain OA [auth C] Focus chain QB [auth P] Focus chain TA [auth C]
DMU Query on DMU Download:Ideal Coordinates CCD File SDF format, chain BB [auth M] SDF format, chain BC [auth Z] MOL2 format, chain BB [auth M] MOL2 format, chain BC [auth Z] mmCIF format, chain BB [auth M] mmCIF format, chain BC [auth Z]	BB [auth M], BC [auth Z]	DECYL-BETA-D-MALTOPYRANOSIDE C₂₂ H₄₂ O₁₁ WOQQAWHSKSSAGF-WXFJLFHKSA-N		Interactions Focus chain BB [auth M] Focus chain BC [auth Z] Interactions & Density Focus chain BB [auth M] Focus chain BC [auth Z]
CHD Query on CHD Download:Ideal Coordinates CCD File SDF format, chain KA [auth B] SDF format, chain QA [auth C] SDF format, chain RA [auth C] SDF format, chain SB [auth P] SDF format, chain TB [auth P] SDF format, chain YA [auth G] SDF format, chain ZA [auth J] SDF format, chain ZB [auth W] MOL2 format, chain KA [auth B] MOL2 format, chain QA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain SB [auth P] MOL2 format, chain TB [auth P] MOL2 format, chain YA [auth G] MOL2 format, chain ZA [auth J] MOL2 format, chain ZB [auth W] mmCIF format, chain KA [auth B] mmCIF format, chain QA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain SB [auth P] mmCIF format, chain TB [auth P] mmCIF format, chain YA [auth G] mmCIF format, chain ZA [auth J] mmCIF format, chain ZB [auth W]	KA [auth B] QA [auth C] RA [auth C] SB [auth P] TB [auth P] KA [auth B], QA [auth C], RA [auth C], SB [auth P], TB [auth P], YA [auth G], ZA [auth J], ZB [auth W]	CHOLIC ACID C₂₄ H₄₀ O₅ BHQCQFFYRZLCQQ-OELDTZBJSA-N		Interactions Focus chain KA [auth B] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SB [auth P] Focus chain TB [auth P] Focus chain YA [auth G] Focus chain ZA [auth J] Focus chain ZB [auth W] Interactions & Density Focus chain KA [auth B] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SB [auth P] Focus chain TB [auth P] Focus chain YA [auth G] Focus chain ZA [auth J] Focus chain ZB [auth W]
CUA Query on CUA Download:Ideal Coordinates CCD File SDF format, chain JA [auth B] SDF format, chain MB [auth O] MOL2 format, chain JA [auth B] MOL2 format, chain MB [auth O] mmCIF format, chain JA [auth B] mmCIF format, chain MB [auth O]	JA [auth B], MB [auth O]	DINUCLEAR COPPER ION Cu₂ ALKZAGKDWUSJED-UHFFFAOYSA-N		Interactions Focus chain JA [auth B] Focus chain MB [auth O] Interactions & Density Focus chain JA [auth B] Focus chain MB [auth O]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain VA [auth F] SDF format, chain WB [auth S] MOL2 format, chain VA [auth F] MOL2 format, chain WB [auth S] mmCIF format, chain VA [auth F] mmCIF format, chain WB [auth S]	VA [auth F], WB [auth S]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain VA [auth F] Focus chain WB [auth S] Interactions & Density Focus chain VA [auth F] Focus chain WB [auth S]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain EB [auth N] MOL2 format, chain CA [auth A] MOL2 format, chain EB [auth N] mmCIF format, chain CA [auth A] mmCIF format, chain EB [auth N]	CA [auth A], EB [auth N]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Focus chain EB [auth N] Interactions & Density Focus chain CA [auth A] Focus chain EB [auth N]
PER Query on PER Download:Ideal Coordinates CCD File SDF format, chain FA [auth A] SDF format, chain HB [auth N] MOL2 format, chain FA [auth A] MOL2 format, chain HB [auth N] mmCIF format, chain FA [auth A] mmCIF format, chain HB [auth N]	FA [auth A], HB [auth N]	PEROXIDE ION O₂ ANAIPYUSIMHBEL-UHFFFAOYSA-N		Interactions Focus chain FA [auth A] Focus chain HB [auth N] Interactions & Density Focus chain FA [auth A] Focus chain HB [auth N]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain DA [auth A] SDF format, chain FB [auth N] MOL2 format, chain DA [auth A] MOL2 format, chain FB [auth N] mmCIF format, chain DA [auth A] mmCIF format, chain FB [auth N]	DA [auth A], FB [auth N]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain DA [auth A] Focus chain FB [auth N] Interactions & Density Focus chain DA [auth A] Focus chain FB [auth N]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain EA [auth A] SDF format, chain GB [auth N] SDF format, chain MA [auth C] SDF format, chain OB [auth P] MOL2 format, chain EA [auth A] MOL2 format, chain GB [auth N] MOL2 format, chain MA [auth C] MOL2 format, chain OB [auth P] mmCIF format, chain EA [auth A] mmCIF format, chain GB [auth N] mmCIF format, chain MA [auth C] mmCIF format, chain OB [auth P]	EA [auth A], GB [auth N], MA [auth C], OB [auth P]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain EA [auth A] Focus chain GB [auth N] Focus chain MA [auth C] Focus chain OB [auth P] Interactions & Density Focus chain EA [auth A] Focus chain GB [auth N] Focus chain MA [auth C] Focus chain OB [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: 1.90 Å
R-Value Free: 0.230 (Depositor), 0.248 (DCC)
R-Value Work: 0.195 (Depositor), 0.218 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.6	α = 90
b = 204.51	β = 90
c = 178.29	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
X-PLOR	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2014-04-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-04-30
Type: Initial release
Version 1.1: 2014-06-25
Changes: Database references
Version 1.2: 2018-01-24
Changes: Data collection
Version 1.3: 2022-08-24
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2023-11-08
Changes: Data collection, Refinement description

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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.

3WG7 | pdb_00003wg7

A 1.9 angstrom radiation damage free X-ray structure of large (420KDa) protein by femtosecond crystallography

Literature

Determination of damage-free crystal structure of an X-ray-sensitive protein using an XFEL.

Biological Assembly 1

Biological Assembly 2

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)