3GOQ | pdb_00003goq

Crystal structure of the Tyr13Met variant of Bacillus subtilis ferrochelatase

PDB DOI: https://doi.org/10.2210/pdb3GOQ/pdb

Classification: LYASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2009-03-19 Released: 2010-03-31
Deposition Author(s): Karlberg, T., Hansson, M.D., Hansson, M., Al-Karadaghi, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.232 (Depositor), 0.240 (DCC)
R-Value Work:
0.198 (Depositor), 0.200 (DCC)
R-Value Observed:
0.200 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of the Tyr13Met variant of Bacillus subtilis ferrochelatase

Karlberg, T., Hansson, M.D., Hansson, M., Al-Karadaghi, S.

To be published.

Macromolecule Content

Total Structure Weight: 35.41 kDa
Atom Count: 2,638
Modeled Residue Count: 307
Deposited Residue Count: 310
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferrochelatase	A	310	Bacillus subtilis	Mutation(s): 1 Gene Names: BSU10130, hemF, hemH EC: 4.99.1.1 (PDB Primary Data), 4.99.1.9 (UniProt)
UniProt
Find proteins for P32396 (Bacillus subtilis (strain 168)) Explore P32396 Go to UniProtKB: P32396
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P32396
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.232 (Depositor), 0.240 (DCC)
R-Value Work: 0.198 (Depositor), 0.200 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.33	α = 90
b = 49.9	β = 90
c = 118.05	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
MAR345dtb	data collection
XDS	data reduction
XSCALE	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2010-03-31

Deposition Author(s):

Al-Karadaghi, S.

Revision History (Full details and data files)

Version 1.0: 2010-03-31
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2018-01-24
Changes: Data collection, Structure summary
Version 1.3: 2019-07-24
Changes: Data collection, Refinement description
Version 1.4: 2021-10-20
Changes: Database references, Derived calculations
Version 1.5: 2023-09-06
Changes: Data collection, Refinement description

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.