4ETI | pdb_00004eti

Crystal Structure of YwlE from Bacillus subtilis

PDB DOI: https://doi.org/10.2210/pdb4ETI/pdb

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

Deposited: 2012-04-24 Released: 2012-05-23
Deposition Author(s): Cao, X.F., Brostromer, E., Liu, X.Y., Su, X.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.201 (Depositor), 0.185 (DCC)
R-Value Work:
0.178 (Depositor), 0.171 (DCC)
R-Value Observed:
0.181 (Depositor)

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

Literature

Crystal Structure of YwlE from Bacillus subtilis

Cao, X.F.

To be published.

Macromolecule Content

Total Structure Weight: 20.41 kDa
Atom Count: 1,375
Modeled Residue Count: 150
Deposited Residue Count: 184
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Low molecular weight protein-tyrosine-phosphatase ywlE	A	184	Bacillus subtilis	Mutation(s): 0 Gene Names: ywlE, BSU36930, ipc-31d EC: 3.1.3.48 (PDB Primary Data), 3.9.1.2 (UniProt)
UniProt
Find proteins for P39155 (Bacillus subtilis (strain 168)) Explore P39155 Go to UniProtKB: P39155
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P39155
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.201 (Depositor), 0.185 (DCC)
R-Value Work: 0.178 (Depositor), 0.171 (DCC)
R-Value Observed: 0.181 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.736	α = 90
b = 38.764	β = 91.12
c = 40.463	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHENIX	model building
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-05-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-05-23
Type: Initial release
Version 1.1: 2023-11-08
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.