4JOU | pdb_00004jou

Structural study of Bacillus subtilis HmoB in complex with heme

PDB DOI: https://doi.org/10.2210/pdb4JOU/pdb

Classification: ANTIBIOTIC
Organism(s): Bacillus spizizenii str. W23
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-03-19 Released: 2014-03-19
Deposition Author(s): Choe, J., Park, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.280 (Depositor), 0.280 (DCC)
R-Value Work:
0.195 (Depositor), 0.200 (DCC)
R-Value Observed:
0.199 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural study of Bacillus subtilis HmoB in complex with heme

Choe, J., Park, S.

To be published.

Macromolecule Content

Total Structure Weight: 19.48 kDa
Atom Count: 1,351
Modeled Residue Count: 155
Deposited Residue Count: 166
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein yhgC	A	166	Bacillus spizizenii str. W23	Mutation(s): 0 Gene Names: yhgC, BSUW23_05110
UniProt
Find proteins for E0TXX3 (Bacillus spizizenii (strain ATCC 23059 / NRRL B-14472 / W23)) Explore E0TXX3 Go to UniProtKB: E0TXX3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E0TXX3
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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.280 (Depositor), 0.280 (DCC)
R-Value Work: 0.195 (Depositor), 0.200 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.597	α = 90
b = 99.597	β = 90
c = 99.597	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-03-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-03-19
Type: Initial release
Version 1.1: 2024-03-20
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.