3QBL | pdb_00003qbl

Pharaonis halorhodopsin complexed with nitrate

PDB DOI: https://doi.org/10.2210/pdb3QBL/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Natronomonas pharaonis
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2011-01-13 Released: 2011-08-31
Deposition Author(s): Kouyama, T., Kanada, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.267 (Depositor), 0.260 (DCC)
R-Value Work:
0.252 (Depositor), 0.250 (DCC)
R-Value Observed:
0.262 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structures of anion-free blue and yellow forms of pharaonis halorhodopsin

Kanada, S., Takeguchi, Y., Murakami, M., Ihara, K., Kouyama, T.

To be published.

Macromolecule Content

Total Structure Weight: 95.63 kDa
Atom Count: 6,151
Modeled Residue Count: 778
Deposited Residue Count: 873
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Halorhodopsin	A, B, C [auth D]	291	Natronomonas pharaonis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P15647 (Natronomonas pharaonis) Explore P15647 Go to UniProtKB: P15647
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P15647
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
22B Query on 22B Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain L [auth D] MOL2 format, chain I [auth B] MOL2 format, chain L [auth D] mmCIF format, chain I [auth B] mmCIF format, chain L [auth D]	I [auth B], L [auth D]	BACTERIORUBERIN C₅₀ H₇₆ O₄ UVCQMCCIAHQDAF-CUMPQFAQSA-N		Interactions Focus chain I [auth B] Focus chain L [auth D] Interactions & Density Focus chain I [auth B] Focus chain L [auth D]
RET Query on RET Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain K [auth D] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth D] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth D]	D [auth A], H [auth B], K [auth D]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Focus chain K [auth D] Interactions & Density Focus chain D [auth A] Focus chain H [auth B] Focus chain K [auth D]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth D] SDF format, chain N [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D]	E [auth A] F [auth A] G [auth A] J [auth B] M [auth D] E [auth A], F [auth A], G [auth A], J [auth B], M [auth D], N [auth D]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth D] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth D] Focus chain N [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.267 (Depositor), 0.260 (DCC)
R-Value Work: 0.252 (Depositor), 0.250 (DCC)
R-Value Observed: 0.262 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.75	α = 90
b = 100.03	β = 127.23
c = 99.33	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-08-31

Deposition Author(s):

Kouyama, T.

Kanada, S.

Revision History (Full details and data files)

Version 1.0: 2011-08-31
Type: Initial release
Version 1.1: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary

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Pharaonis halorhodopsin complexed with nitrate

Crystal structures of anion-free blue and yellow forms of pharaonis halorhodopsin

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations