4FVC | pdb_00004fvc

HmoB structure with heme

• PDB DOI: https://doi.org/10.2210/pdb4FVC/pdb

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


• Deposited: 2012-06-29 Released: 2013-07-03 
• Deposition Author(s): Park, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.233 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Literature

Crystal structure of HmoB with Heme

Park, S.

To be published.

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)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

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

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

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

Biological assembly 6 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 116.63 kDa 
• Atom Count: 8,378 
• Modeled Residue Count: 901 
• Deposited Residue Count: 996 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.233 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.821	α = 90
b = 117.519	β = 91.22
c = 70.847	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
CCP4	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-03 
Deposition Author(s): Park, S.

Revision History  

• Version 1.0: 2013-07-03
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations