4ETM

Crystal structure of YfkJ from Bacillus subtilis

PDB DOI: https://doi.org/10.2210/pdb4ETM/pdb

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

Deposited: 2012-04-24 Released: 2012-10-24
Deposition Author(s): Cao, X.F., Su, X.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.248
R-Value Work: 0.225
R-Value Observed: 0.226

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of YfkJ from Bacillus subtilis

Cao, X.F., Su, X.D.

To be published.

Macromolecule Content

Total Structure Weight: 38.22 kDa
Atom Count: 2,906
Modelled Residue Count: 321
Deposited Residue Count: 346
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Low molecular weight protein-tyrosine-phosphatase yfkJ	A, B	173	Bacillus subtilis	Mutation(s): 0 Gene Names: yfkJ, BSU07880 EC: 3.1.3.48
UniProt
Find proteins for O35016 (Bacillus subtilis (strain 168)) Explore O35016 Go to UniProtKB: O35016
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O35016
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B]	C [auth A], F [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B]	E [auth A], H [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B]	D [auth A], G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.248
R-Value Work: 0.225
R-Value Observed: 0.226
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.152	α = 90
b = 52.922	β = 102.84
c = 86.609	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-10-24

Deposition Author(s):

Cao, X.F.

Su, X.D.

Revision History (Full details and data files)

Version 1.0: 2012-10-24
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description

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4ETM

Crystal structure of YfkJ from Bacillus subtilis

Crystal structure of YfkJ from Bacillus subtilis

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)