1VGO

Crystal Structure of Archaerhodopsin-2

PDB DOI: https://doi.org/10.2210/pdb1VGO/pdb

Classification: PROTON TRANSPORT
Organism(s): Halobacterium sp. AUS-2
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMD

Deposited: 2004-04-28 Released: 2005-10-04
Deposition Author(s): Yoshimura, K., Enami, N., Murakami, M., Okumura, H., Ihara, K., Kouyama, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.268
R-Value Work: 0.241

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 59.16 kDa
Atom Count: 3,956
Modelled Residue Count: 468
Deposited Residue Count: 506
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Archaerhodopsin 2	A, B	253	Halobacterium sp. AUS-2	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P29563 (Halobacterium sp. (strain aus-2)) Explore P29563 Go to UniProtKB: P29563
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P29563
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BNG Query on BNG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], N [auth B], O [auth B], P [auth B]	nonyl beta-D-glucopyranoside C₁₅ H₃₀ O₆ QFAPUKLCALRPLH-UXXRCYHCSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B]
RET Query on RET Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain S [auth B] MOL2 format, chain M [auth A] MOL2 format, chain S [auth B]	M [auth A], S [auth B]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain M [auth A] Focus chain S [auth B] Interactions & Density Focus chain M [auth A] Focus chain S [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B]	L [auth A], Q [auth B], R [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain L [auth A] Focus chain Q [auth B] Focus chain R [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.268
R-Value Work: 0.241
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.88	α = 90
b = 139.48	β = 90
c = 108.1	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CNS	refinement
CCP4	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-10-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-10-04
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2023-10-25
Changes: Data collection, Database references, Refinement description, Structure summary