2HHK

Reaction centre from Rhodobacter sphaeroides strain R-26.1 complexed with dibrominated phosphatidylglycerol

PDB DOI: https://doi.org/10.2210/pdb2HHK/pdb

Classification: PHOTOSYNTHESIS/MEMBRANE PROTEIN
Organism(s): Cereibacter sphaeroides
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2006-06-28 Released: 2007-03-27
Deposition Author(s): Roszak, A.W., Gardiner, A.T., Isaacs, N.W., Cogdell, R.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.197
R-Value Work: 0.172
R-Value Observed: 0.173

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

Brominated Lipids Identify Lipid Binding Sites on the Surface of the Reaction Center from Rhodobacter sphaeroides.

Roszak, A.W., Gardiner, A.T., Isaacs, N.W., Cogdell, R.J.

(2007) Biochemistry 46: 2909-2916

PubMed: 17315985 Search on PubMed
DOI: https://doi.org/10.1021/bi062154i
Primary Citation of Related Structures:
2HG3, 2HG9, 2HH1, 2HHK, 2HIT, 2HJ6

PubMed Abstract:
This study describes the use of brominated phospholipids to distinguish between lipid and detergent binding sites on the surface of a typical alpha-helical membrane protein. Reaction centers isolated from Rhodobacter sphaeroides were cocrystallized with added brominated phospholipids. X-ray structural analysis of these crystals has revealed the presence of two lipid binding sites from the characteristic strong X-ray scattering from the bromine atoms. These results demonstrate the usefulness of this approach to mapping lipid binding sites at the surface of membrane proteins.

Organizational Affiliation

Department of Chemistry, WestCHEM.

Macromolecule Content

Total Structure Weight: 106.34 kDa
Atom Count: 7,824
Modelled Residue Count: 824
Deposited Residue Count: 848
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein L chain	A [auth L]	281	Cereibacter sphaeroides	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0C0Y8 (Cereibacter sphaeroides) Explore P0C0Y8 Go to UniProtKB: P0C0Y8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C0Y8
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 M chain	B [auth M]	307	Cereibacter sphaeroides	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0C0Y9 (Cereibacter sphaeroides) Explore P0C0Y9 Go to UniProtKB: P0C0Y9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C0Y9
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 H chain	C [auth H]	260	Cereibacter sphaeroides	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P0C0Y7 (Cereibacter sphaeroides) Explore P0C0Y7 Go to UniProtKB: P0C0Y7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0C0Y7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 12 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CDL Query on CDL Download Ideal Coordinates CCD File SDF format, chain T [auth M] MOL2 format, chain T [auth M] mmCIF format, chain T [auth M]	T [auth M]	CARDIOLIPIN C₈₁ H₁₅₆ O₁₇ P₂ XVTUQDWPJJBEHJ-KZCWQMDCSA-L		Interactions Focus chain T [auth M] Interactions & Density Focus chain T [auth M]
BCL Query on BCL Download Ideal Coordinates CCD File SDF format, chain D [auth L] SDF format, chain E [auth L] SDF format, chain P [auth M] SDF format, chain Q [auth M] MOL2 format, chain D [auth L] MOL2 format, chain E [auth L] MOL2 format, chain P [auth M] MOL2 format, chain Q [auth M] mmCIF format, chain D [auth L] mmCIF format, chain E [auth L] mmCIF format, chain P [auth M] mmCIF format, chain Q [auth M]	D [auth L], E [auth L], P [auth M], Q [auth M]	BACTERIOCHLOROPHYLL A C₅₅ H₇₄ Mg N₄ O₆ DSJXIQQMORJERS-AGGZHOMASA-M		Interactions Focus chain D [auth L] Focus chain E [auth L] Focus chain P [auth M] Focus chain Q [auth M] Interactions & Density Focus chain D [auth L] Focus chain E [auth L] Focus chain P [auth M] Focus chain Q [auth M]
PGK Query on PGK Download Ideal Coordinates CCD File SDF format, chain U [auth M] MOL2 format, chain U [auth M] mmCIF format, chain U [auth M]	U [auth M]	(1R)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (9S,10S)-9,10-DIBROMOOCTADECANOATE C₄₀ H₇₇ Br₂ O₁₀ P SZYLEOPJERUXOZ-RNATXAOGSA-N		Interactions Focus chain U [auth M] Interactions & Density Focus chain U [auth M]
BPH Query on BPH Download Ideal Coordinates CCD File SDF format, chain F [auth L] SDF format, chain R [auth M] MOL2 format, chain F [auth L] MOL2 format, chain R [auth M] mmCIF format, chain F [auth L] mmCIF format, chain R [auth M]	F [auth L], R [auth M]	BACTERIOPHEOPHYTIN A C₅₅ H₇₆ N₄ O₆ KWOZSBGNAHVCKG-SZQBJALDSA-N		Interactions Focus chain F [auth L] Focus chain R [auth M] Interactions & Density Focus chain F [auth L] Focus chain R [auth M]
U10 Query on U10 Download Ideal Coordinates CCD File SDF format, chain G [auth L] SDF format, chain S [auth M] MOL2 format, chain G [auth L] MOL2 format, chain S [auth M] mmCIF format, chain G [auth L] mmCIF format, chain S [auth M]	G [auth L], S [auth M]	UBIQUINONE-10 C₅₉ H₉₀ O₄ ACTIUHUUMQJHFO-UPTCCGCDSA-N		Interactions Focus chain G [auth L] Focus chain S [auth M] Interactions & Density Focus chain G [auth L] Focus chain S [auth M]
PGT Query on PGT Download Ideal Coordinates CCD File SDF format, chain AA [auth H] MOL2 format, chain AA [auth H] mmCIF format, chain AA [auth H]	AA [auth H]	(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE C₄₀ H₇₉ O₁₀ P KBPVYRBBONZJHF-AMAPPZPBSA-N		Interactions Focus chain AA [auth H] Interactions & Density Focus chain AA [auth H]
LDA Query on LDA Download Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain CA [auth H] SDF format, chain DA [auth H] SDF format, chain V [auth M] SDF format, chain W [auth M] SDF format, chain X [auth M] MOL2 format, chain BA [auth H] MOL2 format, chain CA [auth H] MOL2 format, chain DA [auth H] MOL2 format, chain V [auth M] MOL2 format, chain W [auth M] MOL2 format, chain X [auth M] mmCIF format, chain BA [auth H] mmCIF format, chain CA [auth H] mmCIF format, chain DA [auth H] mmCIF format, chain V [auth M] mmCIF format, chain W [auth M] mmCIF format, chain X [auth M]	BA [auth H] CA [auth H] DA [auth H] V [auth M] W [auth M] BA [auth H], CA [auth H], DA [auth H], V [auth M], W [auth M], X [auth M]	LAURYL DIMETHYLAMINE-N-OXIDE C₁₄ H₃₁ N O SYELZBGXAIXKHU-UHFFFAOYSA-N		Interactions Focus chain BA [auth H] Focus chain CA [auth H] Focus chain DA [auth H] Focus chain V [auth M] Focus chain W [auth M] Focus chain X [auth M] Interactions & Density Focus chain BA [auth H] Focus chain CA [auth H] Focus chain DA [auth H] Focus chain V [auth M] Focus chain W [auth M] Focus chain X [auth M]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain M SDF format, chain N [auth M] SDF format, chain O [auth M] SDF format, chain Z [auth H] MOL2 format, chain M MOL2 format, chain N [auth M] MOL2 format, chain O [auth M] MOL2 format, chain Z [auth H] mmCIF format, chain M mmCIF format, chain N [auth M] mmCIF format, chain O [auth M] mmCIF format, chain Z [auth H]	M, N [auth M], O [auth M], Z [auth H]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain M Focus chain N [auth M] Focus chain O [auth M] Focus chain Z [auth H] Interactions & Density Focus chain M Focus chain N [auth M] Focus chain O [auth M] Focus chain Z [auth H]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain EA [auth H] SDF format, chain H [auth L] SDF format, chain I [auth L] SDF format, chain J [auth L] MOL2 format, chain EA [auth H] MOL2 format, chain H [auth L] MOL2 format, chain I [auth L] MOL2 format, chain J [auth L] mmCIF format, chain EA [auth H] mmCIF format, chain H [auth L] mmCIF format, chain I [auth L] mmCIF format, chain J [auth L]	EA [auth H], H [auth L], I [auth L], J [auth L]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth H] Focus chain H [auth L] Focus chain I [auth L] Focus chain J [auth L] Interactions & Density Focus chain EA [auth H] Focus chain H [auth L] Focus chain I [auth L] Focus chain J [auth L]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain K [auth M] MOL2 format, chain K [auth M] mmCIF format, chain K [auth M]	K [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain K [auth M] Interactions & Density Focus chain K [auth M]
K Query on K Download Ideal Coordinates CCD File SDF format, chain Y [auth H] MOL2 format, chain Y [auth H] mmCIF format, chain Y [auth H]	Y [auth H]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain Y [auth H] Interactions & Density Focus chain Y [auth H]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain L [auth M] MOL2 format, chain L [auth M] mmCIF format, chain L [auth M]	L [auth M]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth M] Interactions & Density Focus chain L [auth M]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.197
R-Value Work: 0.172
R-Value Observed: 0.173
Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.417	α = 90
b = 139.417	β = 90
c = 183.701	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-03-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-03-27
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.3: 2018-01-31
Changes: Experimental preparation
Version 1.4: 2018-02-28
Changes: Experimental preparation
Version 1.5: 2024-02-14
Changes: Data collection, Database references, Derived calculations
Version 1.6: 2024-04-03
Changes: Refinement description