3M4Z

Crystal Structure of B. subtilis ferrochelatase with Cobalt bound at the active site

PDB DOI: https://doi.org/10.2210/pdb3M4Z/pdb

Classification: LYASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-03-12 Released: 2010-11-10
Deposition Author(s): Soderberg, C.A.G., Hansson, M.D., Sreekanth, R., Al-Karadaghi, S., Hansson, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.199
R-Value Work: 0.168
R-Value Observed: 0.170

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Bacterial ferrochelatase goes human: Tyr13 determines the apparent metal specificity of Bacillus subtilis ferrochelatase

Hansson, M.D., Karlberg, T., Soderberg, C.A.G., Sreekanth, R., Warren, M.J., Al-Karadaghi, S., Rigby, S.E.J., Hansson, M.

To be published.

Macromolecule Content

Total Structure Weight: 35.46 kDa
Atom Count: 2,759
Modelled Residue Count: 309
Deposited Residue Count: 309
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	309	Bacillus subtilis	Mutation(s): 0 Gene Names: hemF, hemH EC: 4.99.1.1
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CO Query on CO Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A]	F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free: 0.199
R-Value Work: 0.168
R-Value Observed: 0.170
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.41	α = 90
b = 49.9	β = 90
c = 118.08	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-11-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-11-10
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2014-11-12
Changes: Structure summary
Version 1.3: 2018-05-16
Changes: Data collection
Version 1.4: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

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3M4Z

Crystal Structure of B. subtilis ferrochelatase with Cobalt bound at the active site

Bacterial ferrochelatase goes human: Tyr13 determines the apparent metal specificity of Bacillus subtilis ferrochelatase

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)