6JV6 | pdb_00006jv6

Crystal structure of the sirohydrochlorin chelatase SirB from Bacillus subtilis subspecies spizizenii in complex with cobalt

• PDB DOI: https://doi.org/10.2210/pdb6JV6/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Bacillus spizizenii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-04-16 Released: 2019-06-12 
• Deposition Author(s): Nam, M.S., Song, W.S., Park, S.C., Yoon, S.I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.248 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Cobalt complex structure of the sirohydrochlorin chelatase SirB from Bacillus subtilis subsp. spizizenii.

Nam, M.S., Song, W.S., Park, S.C., Yoon, S.I.

(2019) Korean J Microbiol 55: 123-130

• DOI: https://doi.org/10.7845/kjm.2019.9042

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 29.43 kDa 
• Atom Count: 1,816 
• Modeled Residue Count: 234 
• Deposited Residue Count: 267 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sirohydrochlorin ferrochelatase	A	267	Bacillus spizizenii	Mutation(s): 0  Gene Names: sirB EC: 4.99.1.3 (PDB Primary Data), 4.99.1.4 (PDB Primary Data)

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO	B [auth A], C [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.248 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.669	α = 90
b = 75.669	β = 90
c = 82.419	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-06-12 
Deposition Author(s): Nam, M.S., Song, W.S., Park, S.C., Yoon, S.I.

Revision History  

• Version 1.0: 2019-06-12
  Type: Initial release
  
• Version 1.1: 2019-11-13
  Changes: Database references
• Version 1.2: 2019-11-20
  Changes: Database references, Derived calculations
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description