2JBL

PHOTOSYNTHETIC REACTION CENTER FROM BLASTOCHLORIS VIRIDIS

PDB DOI: https://doi.org/10.2210/pdb2JBL/pdb
Entry: 2JBL supersedes: 4PRC

Classification: ELECTRON TRANSPORT
Organism(s): Blastochloris viridis
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2006-12-08 Released: 2007-03-13
Deposition Author(s): Lancaster, C.R.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.206
R-Value Work: 0.190
R-Value Observed: 0.190

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

A Comparison of Stigmatellin Conformations, Free and Bound to the Photosynthetic Reaction Center and the Cytochrome Bc(1) Complex.

Lancaster, C.R.D., Hunte, C., Kelley, J., Trumpower, B.L., Ditchfield, R.

(2007) J Mol Biol 368: 197

PubMed: 17337272 Search on PubMed
DOI: https://doi.org/10.1016/j.jmb.2007.02.013
Primary Citation of Related Structures:
2IBZ, 2JBL

PubMed Abstract:
We describe in detail the conformations of the inhibitor stigmatellin in its free form and bound to the ubiquinone-reducing (Q(B)) site of the reaction center and to the ubiquinol-oxidizing (Q(o)) site of the cytochrome bc(1) complex. We present here the first structures of a stereochemically correct stigmatellin in complexes with a bacterial reaction center and the yeast cytochrome bc1 complex. The conformations of the inhibitor bound to the two enzymes are not the same. We focus on the orientations of the stigmatellin side-chain relative to the chromone head group, and on the interaction of the stigmatellin side-chain with these membrane protein complexes. The different conformations of stigmatellin found illustrate the structural variability of the Q sites, which are affected by the same inhibitor. The free rotation about the chi1 dihedral angle is an essential factor for allowing stigmatellin to bind in both the reaction center and the cytochrome bc1 pocket.

Organizational Affiliation

Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, D-60438 Frankfurt, Germany. Roy.Lancaster@mpibp-frankfurt.mpg.de

Macromolecule Content

Total Structure Weight: 145.79 kDa
Atom Count: 10,512
Modelled Residue Count: 1,186
Deposited Residue Count: 1,210
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT	A [auth C]	356	Blastochloris viridis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P07173 (Blastochloris viridis) Explore P07173 Go to UniProtKB: P07173
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07173
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
REACTION CENTER PROTEIN H CHAIN	B [auth H]	258	Blastochloris viridis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P06008 (Blastochloris viridis) Explore P06008 Go to UniProtKB: P06008
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06008
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
REACTION CENTER PROTEIN L CHAIN	C [auth L]	273	Blastochloris viridis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P06009 (Blastochloris viridis) Explore P06009 Go to UniProtKB: P06009
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06009
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
REACTION CENTER PROTEIN M CHAIN	D [auth M]	323	Blastochloris viridis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P06010 (Blastochloris viridis) Explore P06010 Go to UniProtKB: P06010
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06010
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCB Query on BCB Download Ideal Coordinates CCD File SDF format, chain K [auth L] SDF format, chain L SDF format, chain O [auth L] SDF format, chain P [auth M] MOL2 format, chain K [auth L] MOL2 format, chain L MOL2 format, chain O [auth L] MOL2 format, chain P [auth M]	K [auth L], L, O [auth L], P [auth M]	BACTERIOCHLOROPHYLL B C₅₅ H₇₂ Mg N₄ O₆ QNWPCDKNPGOYNP-DSENBSCCSA-M		Interactions Focus chain K [auth L] Focus chain L Focus chain O [auth L] Focus chain P [auth M] Interactions & Density Focus chain K [auth L] Focus chain L Focus chain O [auth L] Focus chain P [auth M]
BPB Query on BPB Download Ideal Coordinates CCD File SDF format, chain M [auth L] SDF format, chain Q [auth M] MOL2 format, chain M [auth L] MOL2 format, chain Q [auth M]	M [auth L], Q [auth M]	BACTERIOPHEOPHYTIN B C₅₅ H₇₄ N₄ O₆ SFKCKJXMIAKQMY-GTTFDWDMSA-N		Interactions Focus chain M [auth L] Focus chain Q [auth M] Interactions & Density Focus chain M [auth L] Focus chain Q [auth M]
MQ7 Query on MQ7 Download Ideal Coordinates CCD File SDF format, chain S [auth M] MOL2 format, chain S [auth M]	S [auth M]	MENAQUINONE-7 C₄₆ H₆₄ O₂ RAKQPZMEYJZGPI-LJWNYQGCSA-N		Interactions Focus chain S [auth M] Interactions & Density Focus chain S [auth M]
HEC Query on HEC Download Ideal Coordinates CCD File SDF format, chain E [auth C] SDF format, chain F [auth C] SDF format, chain G [auth C] SDF format, chain H [auth C] MOL2 format, chain E [auth C] MOL2 format, chain F [auth C] MOL2 format, chain G [auth C] MOL2 format, chain H [auth C]	E [auth C], F [auth C], G [auth C], H [auth C]	HEME C C₃₄ H₃₄ Fe N₄ O₄ HXQIYSLZKNYNMH-LJNAALQVSA-N		Interactions Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth C] Interactions & Density Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth C]
NS5 Query on NS5 Download Ideal Coordinates CCD File SDF format, chain T [auth M] MOL2 format, chain T [auth M]	T [auth M]	15-cis-1,2-dihydroneurosporene C₄₀ H₆₀ NHKJSVKSSGKUCH-DBWJSHEJSA-N		Interactions Focus chain T [auth M] Interactions & Density Focus chain T [auth M]
SMA Query on SMA Download Ideal Coordinates CCD File SDF format, chain N [auth L] MOL2 format, chain N [auth L]	N [auth L]	STIGMATELLIN A C₃₀ H₄₂ O₇ UZHDGDDPOPDJGM-WPPYOTIYSA-N		Interactions Focus chain N [auth L] Interactions & Density Focus chain N [auth L]
LDA Query on LDA Download Ideal Coordinates CCD File SDF format, chain U [auth M] SDF format, chain V [auth M] SDF format, chain W [auth M] SDF format, chain X [auth M] SDF format, chain I [auth H] SDF format, chain Y [auth M] MOL2 format, chain U [auth M] MOL2 format, chain V [auth M] MOL2 format, chain W [auth M] MOL2 format, chain X [auth M] MOL2 format, chain I [auth H] MOL2 format, chain Y [auth M]	I [auth H] U [auth M] V [auth M] W [auth M] X [auth M] I [auth H], U [auth M], V [auth M], W [auth M], X [auth M], Y [auth M]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain I [auth H] Focus chain U [auth M] Focus chain V [auth M] Focus chain W [auth M] Focus chain X [auth M] Focus chain Y [auth M] Interactions & Density Focus chain I [auth H] Focus chain U [auth M] Focus chain V [auth M] Focus chain W [auth M] Focus chain X [auth M] Focus chain Y [auth M]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth M] SDF format, chain BA [auth M] SDF format, chain J [auth H] SDF format, chain Z [auth M] MOL2 format, chain AA [auth M] MOL2 format, chain BA [auth M] MOL2 format, chain J [auth H] MOL2 format, chain Z [auth M]	AA [auth M], BA [auth M], J [auth H], Z [auth M]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth M] Focus chain BA [auth M] Focus chain J [auth H] Focus chain Z [auth M] Interactions & Density Focus chain AA [auth M] Focus chain BA [auth M] Focus chain J [auth H] Focus chain Z [auth M]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain R [auth M] MOL2 format, chain R [auth M]	R [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain R [auth M] Interactions & Density Focus chain R [auth M]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME Query on FME	B [auth H]	L-PEPTIDE LINKING	C₆ H₁₁ N O₃ S		MET

Binding Affinity Annotations
ID	Source	Binding Affinity
SMA	PDBBind: 2JBL	IC50: 1300 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.206
R-Value Work: 0.190
R-Value Observed: 0.190
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 223.5	α = 90
b = 223.5	β = 90
c = 113.6	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-03-13

Deposition Author(s):

Lancaster, C.R.D.

This entry supersedes: 4PRC

Revision History (Full details and data files)

Version 1.0: 2007-03-13
Type: Initial release
Version 1.1: 2012-02-01
Changes: Derived calculations, Non-polymer description, Version format compliance
Version 1.2: 2014-10-22
Changes: Database references
Version 1.3: 2019-07-24
Changes: Advisory, Data collection, Derived calculations
Version 2.0: 2019-09-25
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
Version 2.1: 2023-12-13
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description