3TVZ | pdb_00003tvz

Structure of Bacillus subtilis HmoB

• PDB DOI: https://doi.org/10.2210/pdb3TVZ/pdb

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


• Deposited: 2011-09-21 Released: 2012-07-11 
• Deposition Author(s): Choe, J., Choi, S., Park, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.251 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.197 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Literature

Bacillus subtilis HmoB is a heme oxygenase with a novel structure.

Park, S., Choi, S., Choe, J.

(2012) BMB Rep 45: 239-241

• PubMed: 22531134 
• DOI: https://doi.org/10.5483/bmbrep.2012.45.4.239
• Primary Citation Related Structures: 
  3TVZ


• PubMed Abstract: 
  

  Iron availability is limited in the environment and most bacteria have developed a system to acquire iron from host hemoproteins. Heme oxygenase plays an important role by degrading heme group and releasing the essential nutrient iron. The structure of Bacillus subtilis HmoB was determined to 2.0 A resolution. B. subtilis HmoB contains a typical antibiotic biosynthesis monooxygenase (ABM) domain that spans from 71 to 146 residues and belongs to the IsdG family heme oxygenases. Comparison of HmoB and IsdG family proteins showed that the C-terminal region of HmoB has similar sequence and structure to IsdG family proteins and contains conserved critical residues for heme degradation. However, HmoB is distinct from other IsdG family proteins in that HmoB is about 60 amino acids longer in the N-terminus and does not form a dimer whereas previously studied IsdG family heme oxygenases form functional homodimers. Interestingly, the structure of monomeric HmoB resembles the dimeric structure of IsdG family proteins. Hence, B. subtilis HmoB is a heme oxygenase with a novel structural feature.

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Organizational Affiliation: 
• Department of Life Science, University of Seoul, Seoul, Korea.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 58.53 kDa 
• Atom Count: 3,735 
• Modeled Residue Count: 425 
• Deposited Residue Count: 516 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein yhgC	A, B, C	172	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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.251 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.197 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.799	α = 90
b = 64.799	β = 90
c = 392.591	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-11 
Deposition Author(s): Choe, J., Choi, S., Park, S.

Revision History  

• Version 1.0: 2012-07-11
  Type: Initial release
  
• Version 1.1: 2012-07-18
  Changes: Structure summary
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2019-10-09
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Structure summary