5V3V | pdb_00005v3v

Crystal Structure of the Group II Truncated Hemoglobin from Bacillus Anthracis: Tyr26Ala Mutant

PDB DOI: https://doi.org/10.2210/pdb5V3V/pdb

Classification: OXYGEN TRANSPORT
Organism(s): Bacillus anthracis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2017-03-08 Released: 2017-04-12
Deposition Author(s): Varnado, C.L., SoRelle, E., Soman, J., Olson, J.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free:
0.232 (Depositor), 0.228 (DCC)
R-Value Work:
0.211 (Depositor)
R-Value Observed:
0.213 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Crystal Structure of the Group II Truncated Hemoglobin from Bacillus Anthracis

Varnado, C.L., SoRelle, E., Soman, J., Olson, J.S.

To be published.

Macromolecule Content

Total Structure Weight: 31.63 kDa
Atom Count: 2,263
Modeled Residue Count: 253
Deposited Residue Count: 264
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Globin	A, B	132	Bacillus anthracis	Mutation(s): 1 Gene Names: yjbI, GBAA_1209, BASH2_04647, BVB96_06425
UniProt
Find proteins for A0A6L7H965 (Bacillus anthracis) Explore A0A6L7H965 Go to UniProtKB: A0A6L7H965
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A6L7H965
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B]	E [auth A], F [auth A], I [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B]
CYN Query on CYN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.14 Å
R-Value Free: 0.232 (Depositor), 0.228 (DCC)
R-Value Work: 0.211 (Depositor)
R-Value Observed: 0.213 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.449	α = 90
b = 122.303	β = 90
c = 111.494	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
d*TREK	data scaling
d*TREK	data reduction
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-04-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2017-04-12
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2024-03-06
Changes: Data collection, Database references

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.