5ZT9 | pdb_00005zt9

SirB from Bacillus subtilis with Ni2+

PDB DOI: https://doi.org/10.2210/pdb5ZT9/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.245 (Depositor), 0.245 (DCC)
R-Value Work:
0.212 (Depositor), 0.213 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

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

Fujishiro, T.

To be published.

Macromolecule Content

Total Structure Weight: 60.71 kDa
Atom Count: 4,043
Modeled Residue Count: 510
Deposited Residue Count: 546
Unique protein chains: 1

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O34632
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth B], F [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.245 (Depositor), 0.245 (DCC)
R-Value Work: 0.212 (Depositor), 0.213 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.73	α = 90
b = 53.7	β = 107.66
c = 78.02	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-06-12

Deposition Author(s):

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

Revision History (Full details and data files)

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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.