5D1V | pdb_00005d1v

Crystal Structure and Thermal Stability of Hemoglobin from Thermophilic Phototrophic Bacterium Chloroflexus aurantiacus

PDB DOI: https://doi.org/10.2210/pdb5D1V/pdb

Classification: OXYGEN TRANSPORT
Organism(s): Chloroflexus aurantiacus J-10-fl
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-08-04 Released: 2016-08-10
Deposition Author(s): Fromme, R., Holl, M., Tang, J.K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free:
0.187 (Depositor), 0.190 (DCC)
R-Value Work:
0.149 (Depositor), 0.150 (DCC)
R-Value Observed:
0.151 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure and Thermal Stability of Hemoglobin from Thermophilic Phototrophic Bacterium Chloroflexus aurantiacus

Fromme, R., Holl, M., Tang, J.K.

To be published.

Macromolecule Content

Total Structure Weight: 30.98 kDa
Atom Count: 2,553
Modeled Residue Count: 242
Deposited Residue Count: 254
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Globin	A, B	127	Chloroflexus aurantiacus J-10-fl	Mutation(s): 0 Gene Names: Caur_0123
UniProt
Find proteins for A9WBH0 (Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl)) Explore A9WBH0 Go to UniProtKB: A9WBH0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9WBH0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.74 Å
R-Value Free: 0.187 (Depositor), 0.190 (DCC)
R-Value Work: 0.149 (Depositor), 0.150 (DCC)
R-Value Observed: 0.151 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.96	α = 90
b = 41.298	β = 107.7
c = 72.117	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-08-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-08-10
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references, Derived calculations

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.