5ZTA | pdb_00005zta

SirB from Bacillus subtilis with Fe3+

• PDB DOI: https://doi.org/10.2210/pdb5ZTA/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Bacillus subtilis subsp. subtilis str. 168
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-05-02 Released: 2019-06-12 
• Deposition Author(s): Fujishiro, T.
• Funding Organization(s): Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.07 Å
• R-Value Free: 
  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

A route for metal acquisition for chelatase reaction catalyzed by SirB from Bacillus subtilis

Fujishiro, T.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 60.59 kDa 
• Atom Count: 3,967 
• Modeled Residue Count: 506 
• Deposited Residue Count: 546 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sirohydrochlorin ferrochelatase	A, B	273	Bacillus subtilis subsp. subtilis str. 168	Mutation(s): 0  Gene Names: sirB, ylnE, BSU15620 EC: 4.99.1.4
UniProt
Find proteins for O34632 (Bacillus subtilis (strain 168)) Explore O34632  Go to UniProtKB:  O34632

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FE	C [auth A], D [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.07 Å
• R-Value Free:  0.267 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.46	α = 90
b = 53.43	β = 105.8
c = 79.86	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-06-12 
Deposition Author(s): Fujishiro, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science	Japan	17K14510

Revision History  

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