4EGS | pdb_00004egs

Crystal Structure Analysis of Low Molecular Weight Protein Tyrosine Phosphatase from T. tengcongensis

PDB DOI: https://doi.org/10.2210/pdb4EGS/pdb

Classification: ISOMERASE
Organism(s): Caldanaerobacter subterraneus subsp. tengcongensis MB4
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-04-01 Released: 2012-10-03
Deposition Author(s): Cao, X.F., Liu, X.Y., Li, L.F., Su, X.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.212 (Depositor), 0.218 (DCC)
R-Value Work:
0.193 (Depositor), 0.195 (DCC)
R-Value Observed:
0.195 (Depositor)

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

Literature

Crystal Structure Analysis of Low Molecular Weight Protein Tyrosine Phosphatase from T. tengcongensis

Cao, X.F., Liu, X.Y., Li, L.F., Su, X.D.

To be published.

Macromolecule Content

Total Structure Weight: 39.6 kDa
Atom Count: 2,441
Modeled Residue Count: 294
Deposited Residue Count: 360
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribose 5-phosphate isomerase RpiB	A, B	180	Caldanaerobacter subterraneus subsp. tengcongensis MB4	Mutation(s): 0 Gene Names: RpiB, TTE0146
UniProt
Find proteins for Q8RD95 (Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4)) Explore Q8RD95 Go to UniProtKB: Q8RD95
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8RD95
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BCT Query on BCT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.212 (Depositor), 0.218 (DCC)
R-Value Work: 0.193 (Depositor), 0.195 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.964	α = 90
b = 33.176	β = 90.05
c = 117.41	γ = 90

Software Package:

Software Name	Purpose
ADSC	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: 2012-10-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-10-03
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.