8C88 | pdb_00008c88

Double mutant G(M19)C/T(L214)C structure of Photosynthetic Reaction Center From Cereibacter sphaeroides strain RV

PDB DOI: https://doi.org/10.2210/pdb8C88/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Cereibacter sphaeroides 2.4.1
Expression System: Cereibacter sphaeroides 2.4.1
Mutation(s): Yes
Membrane Protein: Yes PDBTM mpstruc

Deposited: 2023-01-19 Released: 2023-11-22
Deposition Author(s): Gabdulkhakov, A., Selikhanov, G., Fufina, T., Vasilieva, L., Atamas, A., Yukhimchuk, D.
Funding Organization(s): Russian Foundation for Basic Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.271 (Depositor), 0.247 (DCC)
R-Value Work:
0.199 (Depositor)
R-Value Observed:
0.202 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Stabilization of Cereibacter sphaeroides Photosynthetic Reaction Center by the Introduction of Disulfide Bonds.

Selikhanov, G., Atamas, A., Yukhimchuk, D., Fufina, T., Vasilieva, L., Gabdulkhakov, A.

(2023) Membranes (Basel) 13

PubMed: 36837657 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3390/membranes13020154
Primary Citation Related Structures:
8C5X, 8C6K, 8C7C, 8C87, 8C88

PubMed Abstract:
The photosynthetic reaction center of the purple nonsulfur bacterium Cereibacter sphaeroides is a useful model for the study of mechanisms of photoinduced electron transfer and a promising component for photo-bio-electrocatalytic systems. The basic research and technological applications of this membrane pigment-protein complex require effective approaches to increase its structural stability. In this work, a rational design approach to genetically modify the reaction centers by introducing disulfide bonds is used. This resulted in significantly increasing the thermal stability of some of the mutant pigment-protein complexes. The formation of the S-S bonds was confirmed by X-ray crystallography as well as SDS-PAGE, and the optical properties of the reaction centers were studied. The genetically modified reaction centers presented here preserved their ability for photochemical charge separation and could be of interest for basic science and biotechnology.

Organizational Affiliation

Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290 Pushchino, Moscow Region, Russia.

Macromolecule Content

Total Structure Weight: 101.72 kDa
Atom Count: 7,341
Modeled Residue Count: 826
Deposited Residue Count: 826
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein H chain	A [auth H]	242	Cereibacter sphaeroides 2.4.1	Mutation(s): 0 Gene Names: puhA Membrane Entity: Yes
UniProt
Find proteins for Q3J170 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3J170 Go to UniProtKB: Q3J170
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3J170
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein L chain	B [auth L]	281	Cereibacter sphaeroides 2.4.1	Mutation(s): 2 Gene Names: pufL Membrane Entity: Yes
UniProt
Find proteins for Q3J1A5 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3J1A5 Go to UniProtKB: Q3J1A5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3J1A5
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	C [auth M]	303	Cereibacter sphaeroides 2.4.1	Mutation(s): 2 Gene Names: pufM Membrane Entity: Yes
UniProt
Find proteins for Q3J1A6 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.)) Explore Q3J1A6 Go to UniProtKB: Q3J1A6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q3J1A6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 12 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCL (Subject of Investigation/LOI) Query on BCL Download:Ideal Coordinates CCD File SDF format, chain J [auth L] SDF format, chain U [auth M] SDF format, chain V [auth M] SDF format, chain K [auth L] MOL2 format, chain J [auth L] MOL2 format, chain U [auth M] MOL2 format, chain V [auth M] MOL2 format, chain K [auth L] mmCIF format, chain J [auth L] mmCIF format, chain U [auth M] mmCIF format, chain V [auth M] mmCIF format, chain K [auth L]	J [auth L], K [auth L], U [auth M], V [auth M]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain J [auth L] Focus chain K [auth L] Focus chain U [auth M] Focus chain V [auth M] Interactions & Density Focus chain J [auth L] Focus chain K [auth L] Focus chain U [auth M] Focus chain V [auth M]
BPH (Subject of Investigation/LOI) Query on BPH Download:Ideal Coordinates CCD File SDF format, chain W [auth M] SDF format, chain L MOL2 format, chain W [auth M] MOL2 format, chain L mmCIF format, chain W [auth M] mmCIF format, chain L	L, W [auth M]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain L Focus chain W [auth M] Interactions & Density Focus chain L Focus chain W [auth M]
U10 (Subject of Investigation/LOI) Query on U10 Download:Ideal Coordinates CCD File SDF format, chain Y [auth M] MOL2 format, chain Y [auth M] mmCIF format, chain Y [auth M]	Y [auth M]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain Y [auth M] Interactions & Density Focus chain Y [auth M]
SPN (Subject of Investigation/LOI) Query on SPN Download:Ideal Coordinates CCD File SDF format, chain Z [auth M] MOL2 format, chain Z [auth M] mmCIF format, chain Z [auth M]	Z [auth M]	SPEROIDENONE C₄₁ H₇₀ O₂ GWQAMGYOEYXWJF-YCDPMLDASA-N		Interactions Focus chain Z [auth M] Interactions & Density Focus chain Z [auth M]
NKP Query on NKP Download:Ideal Coordinates CCD File SDF format, chain D [auth H] SDF format, chain T [auth M] MOL2 format, chain D [auth H] MOL2 format, chain T [auth M] mmCIF format, chain D [auth H] mmCIF format, chain T [auth M]	D [auth H], T [auth M]	(2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate C₂₁ H₄₁ O₇ P WRGQSWVCFNIUNZ-SQUSKLHYSA-N		Interactions Focus chain D [auth H] Focus chain T [auth M] Interactions & Density Focus chain D [auth H] Focus chain T [auth M]
OLC (Subject of Investigation/LOI) Query on OLC Download:Ideal Coordinates CCD File SDF format, chain I [auth L] MOL2 format, chain I [auth L] mmCIF format, chain I [auth L]	I [auth L]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain I [auth L] Interactions & Density Focus chain I [auth L]
LDA Query on LDA Download:Ideal Coordinates CCD File SDF format, chain DA [auth M] SDF format, chain HA [auth M] SDF format, chain E [auth H] SDF format, chain CA [auth M] SDF format, chain BA [auth M] SDF format, chain AA [auth M] MOL2 format, chain DA [auth M] MOL2 format, chain HA [auth M] MOL2 format, chain E [auth H] MOL2 format, chain CA [auth M] MOL2 format, chain BA [auth M] MOL2 format, chain AA [auth M] mmCIF format, chain DA [auth M] mmCIF format, chain HA [auth M] mmCIF format, chain E [auth H] mmCIF format, chain CA [auth M] mmCIF format, chain BA [auth M] mmCIF format, chain AA [auth M]	AA [auth M] BA [auth M] CA [auth M] DA [auth M] E [auth H] AA [auth M], BA [auth M], CA [auth M], DA [auth M], E [auth H], HA [auth M]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain AA [auth M] Focus chain BA [auth M] Focus chain CA [auth M] Focus chain DA [auth M] Focus chain E [auth H] Focus chain HA [auth M] Interactions & Density Focus chain AA [auth M] Focus chain BA [auth M] Focus chain CA [auth M] Focus chain DA [auth M] Focus chain E [auth H] Focus chain HA [auth M]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain FA [auth M] SDF format, chain GA [auth M] MOL2 format, chain FA [auth M] MOL2 format, chain GA [auth M] mmCIF format, chain FA [auth M] mmCIF format, chain GA [auth M]	FA [auth M], GA [auth M]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain FA [auth M] Focus chain GA [auth M] Interactions & Density Focus chain FA [auth M] Focus chain GA [auth M]
DIO Query on DIO Download:Ideal Coordinates CCD File SDF format, chain P [auth L] MOL2 format, chain P [auth L] mmCIF format, chain P [auth L]	P [auth L]	1,4-DIETHYLENE DIOXIDE C₄ H₈ O₂ RYHBNJHYFVUHQT-UHFFFAOYSA-N		Interactions Focus chain P [auth L] Interactions & Density Focus chain P [auth L]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain Q [auth L] SDF format, chain R [auth L] SDF format, chain S [auth L] MOL2 format, chain Q [auth L] MOL2 format, chain R [auth L] MOL2 format, chain S [auth L] mmCIF format, chain Q [auth L] mmCIF format, chain R [auth L] mmCIF format, chain S [auth L]	Q [auth L], R [auth L], S [auth L]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain Q [auth L] Focus chain R [auth L] Focus chain S [auth L] Interactions & Density Focus chain Q [auth L] Focus chain R [auth L] Focus chain S [auth L]
FE (Subject of Investigation/LOI) Query on FE Download:Ideal Coordinates CCD File SDF format, chain X [auth M] MOL2 format, chain X [auth M] mmCIF format, chain X [auth M]	X [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain X [auth M] Interactions & Density Focus chain X [auth M]
UNL Query on UNL Download:Ideal Coordinates CCD File	EA [auth M] F [auth H] G [auth H] H M [auth L] EA [auth M], F [auth H], G [auth H], H, M [auth L], N [auth L], O [auth L]	Unknown ligand VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain EA [auth M] Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain M [auth L] Focus chain N [auth L] Focus chain O [auth L] Interactions & Density Focus chain EA [auth M] Focus chain F [auth H] Focus chain G [auth H] Focus chain H Focus chain M [auth L] Focus chain N [auth L] Focus chain O [auth L]