4QID | pdb_00004qid

Crystal structure of Haloquadratum walsbyi bacteriorhodopsin

PDB DOI: https://doi.org/10.2210/pdb4QID/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Haloquadratum walsbyi DSM 16790
Expression System: Escherichia coli
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD mpstruc

Deposited: 2014-05-30 Released: 2015-07-29
Deposition Author(s): Wang, A.H.J., Hsu, M.F., Yang, C.S., Fu, H.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free:
0.229 (Depositor), 0.221 (DCC)
R-Value Work:
0.207 (Depositor), 0.200 (DCC)
R-Value Observed:
0.208 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

An acid-tolerant light-driven proton pump

Wang, A.H.J., Hsu, M.F., Yang, C.S., Fu, H.Y., Cai, C.J., Yi, H.P.

To be published.

Macromolecule Content

Total Structure Weight: 58.02 kDa
Atom Count: 3,661
Modeled Residue Count: 452
Deposited Residue Count: 524
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriorhodopsin-I	A, B	262	Haloquadratum walsbyi DSM 16790	Mutation(s): 0 Gene Names: bop1, bopI, HQ_1014A Membrane Entity: Yes
UniProt
Find proteins for Q18DH8 (Haloquadratum walsbyi (strain DSM 16790 / HBSQ001)) Explore Q18DH8 Go to UniProtKB: Q18DH8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q18DH8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPG Query on MPG Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate C₂₁ H₄₀ O₄ JPJYKWFFJCWMPK-GDCKJWNLSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
RET Query on RET Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B] mmCIF format, chain C [auth A] mmCIF format, chain F [auth B]	C [auth A], F [auth B]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.57 Å
R-Value Free: 0.229 (Depositor), 0.221 (DCC)
R-Value Work: 0.207 (Depositor), 0.200 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 131.939	α = 90
b = 29.799	β = 118.76
c = 124.973	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-07-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-07-29
Type: Initial release
Version 1.1: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary

4QID | pdb_00004qid

Crystal structure of Haloquadratum walsbyi bacteriorhodopsin

Literature

An acid-tolerant light-driven proton pump

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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