6Z1J | pdb_00006z1j

Photosynthetic Reaction Center From Rhodobacter Sphaeroides strain RV LSP co-crystallization with spheroidene

PDB DOI: https://doi.org/10.2210/pdb6Z1J/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Cereibacter sphaeroides
Expression System: Cereibacter sphaeroides
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD mpstruc

Deposited: 2020-05-13 Released: 2020-12-02
Deposition Author(s): Gabdulkhakov, A.G., Fufina, T.Y., Vasilieva, L.G., Betzel, C., Selikhanov, G.K.
Funding Organization(s): Russian Foundation for Basic Research

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.224 (Depositor), 0.225 (DCC)
R-Value Work:
0.188 (Depositor), 0.188 (DCC)
R-Value Observed:
0.190 (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

Novel approaches for the lipid sponge phase crystallization of the Rhodobacter sphaeroides photosynthetic reaction center.

Selikhanov, G., Fufina, T., Vasilieva, L., Betzel, C., Gabdulkhakov, A.

(2020) IUCrJ 7: 1084-1091

PubMed: 33209319 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S2052252520012142
Primary Citation Related Structures:
6Z02, 6Z1J, 6Z27

PubMed Abstract:
With the recent developments in the field of free-electron-laser-based serial femtosecond crystallography, the necessity to obtain a large number of high-quality crystals has emerged. In this work crystallization techniques were selected, tested and optimized for the lipid mesophase crystallization of the Rhodobacter sphaeroides membrane pigment-protein complex, known as the photosynthetic reaction center (RC). Novel approaches for lipid sponge phase crystallization in comparatively large volumes using Hamilton gas-tight glass syringes and plastic pipetting tips are described. An analysis of RC crystal structures obtained by lipid mesophase crystallization revealed non-native ligands that displaced the native electron-transfer cofactors (carotenoid sphero-idene and a ubi-quinone molecule) from their binding pockets. These ligands were identified and were found to be lipids that are major mesophase components. The selection of distinct co-crystallization conditions with the missing cofactors facilitated the restoration of sphero-idene in its binding site.

Organizational Affiliation

Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, Puschino, Moscow region 142290, Russian Federation.

Macromolecule Content

Total Structure Weight: 100.6 kDa
Atom Count: 7,643
Modeled Residue Count: 823
Deposited Residue Count: 824
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]	241	Cereibacter sphaeroides	Mutation(s): 0 Gene Names: puhA Membrane Entity: Yes
UniProt
Find proteins for P0C0Y7 (Cereibacter sphaeroides) Explore P0C0Y7 Go to UniProtKB: P0C0Y7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C0Y7
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	Mutation(s): 0 Gene Names: pufL Membrane Entity: Yes
UniProt
Find proteins for P0C0Y8 (Cereibacter sphaeroides) Explore P0C0Y8 Go to UniProtKB: P0C0Y8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C0Y8
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]	302	Cereibacter sphaeroides	Mutation(s): 0 Gene Names: pufM Membrane Entity: Yes
UniProt
Find proteins for P0C0Y9 (Cereibacter sphaeroides) Explore P0C0Y9 Go to UniProtKB: P0C0Y9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0C0Y9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 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 E [auth L] SDF format, chain F [auth L] SDF format, chain L [auth M] SDF format, chain K [auth M] MOL2 format, chain E [auth L] MOL2 format, chain F [auth L] MOL2 format, chain L [auth M] MOL2 format, chain K [auth M] mmCIF format, chain E [auth L] mmCIF format, chain F [auth L] mmCIF format, chain L [auth M] mmCIF format, chain K [auth M]	E [auth L], F [auth L], K [auth M], L [auth M]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain E [auth L] Focus chain F [auth L] Focus chain K [auth M] Focus chain L [auth M] Interactions & Density Focus chain E [auth L] Focus chain F [auth L] Focus chain K [auth M] Focus chain L [auth M]
BPH (Subject of Investigation/LOI) Query on BPH Download:Ideal Coordinates CCD File SDF format, chain G [auth L] SDF format, chain M MOL2 format, chain G [auth L] MOL2 format, chain M mmCIF format, chain G [auth L] mmCIF format, chain M	G [auth L], M	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain G [auth L] Focus chain M Interactions & Density Focus chain G [auth L] Focus chain M
U10 (Subject of Investigation/LOI) Query on U10 Download:Ideal Coordinates CCD File SDF format, chain O [auth M] MOL2 format, chain O [auth M] mmCIF format, chain O [auth M]	O [auth M]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain O [auth M] Interactions & Density Focus chain O [auth M]
SPN (Subject of Investigation/LOI) Query on SPN Download:Ideal Coordinates CCD File SDF format, chain P [auth M] MOL2 format, chain P [auth M] mmCIF format, chain P [auth M]	P [auth M]	SPEROIDENONE C₄₁ H₇₀ O₂ GWQAMGYOEYXWJF-YCDPMLDASA-N		Interactions Focus chain P [auth M] Interactions & Density Focus chain P [auth M]
NKP Query on NKP Download:Ideal Coordinates CCD File SDF format, chain X [auth M] SDF format, chain Y [auth M] MOL2 format, chain X [auth M] MOL2 format, chain Y [auth M] mmCIF format, chain X [auth M] mmCIF format, chain Y [auth M]	X [auth M], Y [auth M]	(2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate C₂₁ H₄₁ O₇ P WRGQSWVCFNIUNZ-SQUSKLHYSA-N		Interactions Focus chain X [auth M] Focus chain Y [auth M] Interactions & Density Focus chain X [auth M] Focus chain Y [auth M]
OLC Query on OLC Download:Ideal Coordinates CCD File SDF format, chain J [auth L] MOL2 format, chain J [auth L] mmCIF format, chain J [auth L]	J [auth L]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C₂₁ H₄₀ O₄ RZRNAYUHWVFMIP-GDCKJWNLSA-N		Interactions Focus chain J [auth L] Interactions & Density Focus chain J [auth L]
LDA Query on LDA Download:Ideal Coordinates CCD File SDF format, chain D [auth H] SDF format, chain Q [auth M] SDF format, chain R [auth M] SDF format, chain S [auth M] MOL2 format, chain D [auth H] MOL2 format, chain Q [auth M] MOL2 format, chain R [auth M] MOL2 format, chain S [auth M] mmCIF format, chain D [auth H] mmCIF format, chain Q [auth M] mmCIF format, chain R [auth M] mmCIF format, chain S [auth M]	D [auth H], Q [auth M], R [auth M], S [auth M]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain D [auth H] Focus chain Q [auth M] Focus chain R [auth M] Focus chain S [auth M] Interactions & Density Focus chain D [auth H] Focus chain Q [auth M] Focus chain R [auth M] Focus chain S [auth M]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain W [auth M] MOL2 format, chain W [auth M] mmCIF format, chain W [auth M]	W [auth M]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain W [auth M] Interactions & Density Focus chain W [auth M]
FE Query on FE Download:Ideal Coordinates CCD File SDF format, chain N [auth M] MOL2 format, chain N [auth M] mmCIF format, chain N [auth M]	N [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain N [auth M] Interactions & Density Focus chain N [auth M]
UNL Query on UNL Download:Ideal Coordinates CCD File	H [auth L], I [auth L], T [auth M], U [auth M], V [auth M]	Unknown ligand VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain H [auth L] Focus chain I [auth L] Focus chain T [auth M] Focus chain U [auth M] Focus chain V [auth M] Interactions & Density Focus chain H [auth L] Focus chain I [auth L] Focus chain T [auth M] Focus chain U [auth M] Focus chain V [auth M]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.224 (Depositor), 0.225 (DCC)
R-Value Work: 0.188 (Depositor), 0.188 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.89	α = 90
b = 99.89	β = 90
c = 238.52	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-12-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Russian Foundation for Basic Research	Russian Federation	18-02-40008_mega

Revision History (Full details and data files)

Version 1.0: 2020-12-02
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description, Structure summary