3ABW | pdb_00003abw

Crystal structure of pharaonis halorhodopsin in complex with azide ion

PDB DOI: https://doi.org/10.2210/pdb3ABW/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Natronomonas pharaonis DSM 2160
Mutation(s): No

Deposited: 2009-12-24 Released: 2011-02-02
Deposition Author(s): Kouyama, T., Kanada, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.263 (Depositor), 0.262 (DCC)
R-Value Work:
0.242 (Depositor), 0.242 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Binding mode of azide ion to pharaonis halorhodopsin

Kanada, S., Kouyama, T.

To be published.

Macromolecule Content

Total Structure Weight: 103.35 kDa
Atom Count: 6,320
Modeled Residue Count: 778
Deposited Residue Count: 873
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Halorhodopsin	A, B, C [auth D]	291	Natronomonas pharaonis DSM 2160	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
L3P Query on L3P Download:Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A] G [auth A] H [auth A] K [auth B] L [auth B] F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], Q [auth D], R [auth D], S [auth D]	2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE C₄₆ H₉₄ O₁₁ P₂ TZXJQSKPTCRGCA-VZSPAKCESA-L		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D]
22B Query on 22B Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain E [auth A] MOL2 format, chain N [auth B] MOL2 format, chain E [auth A] mmCIF format, chain N [auth B] mmCIF format, chain E [auth A]	E [auth A], N [auth B]	BACTERIORUBERIN C₅₀ H₇₆ O₄ UVCQMCCIAHQDAF-CUMPQFAQSA-N		Interactions Focus chain E [auth A] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain N [auth B]
RET Query on RET Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain P [auth D] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain P [auth D] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain P [auth D] mmCIF format, chain J [auth B]	D [auth A], J [auth B], P [auth D]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Focus chain P [auth D] Interactions & Density Focus chain D [auth A] Focus chain J [auth B] Focus chain P [auth D]
AZI Query on AZI Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain O [auth B] SDF format, chain I [auth A] MOL2 format, chain T [auth D] MOL2 format, chain O [auth B] MOL2 format, chain I [auth A] mmCIF format, chain T [auth D] mmCIF format, chain O [auth B] mmCIF format, chain I [auth A]	I [auth A], O [auth B], T [auth D]	AZIDE ION N₃ IVRMZWNICZWHMI-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain O [auth B] Focus chain T [auth D] Interactions & Density Focus chain I [auth A] Focus chain O [auth B] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.263 (Depositor), 0.262 (DCC)
R-Value Work: 0.242 (Depositor), 0.242 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.09	α = 90
b = 98.79	β = 127.85
c = 100.14	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-02-02

Deposition Author(s):

Kouyama, T.

Kanada, S.

Revision History (Full details and data files)

Version 1.0: 2011-02-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-30
Changes: Structure summary