2VPH | pdb_00002vph

Crystal structure of the human protein tyrosine phosphatase, non- receptor type 4, PDZ domain

PDB DOI: https://doi.org/10.2210/pdb2VPH/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2008-02-29 Released: 2008-03-18
Deposition Author(s): Roos, A.K., Wang, J., Burgess-Brown, N., Elkins, J.M., Kavanagh, K., Pike, A.C.W., Filippakopoulos, P., Arrowsmith, C.H., Weigelt, J., Edwards, A., von Delft, F., Bountra, C., Knapp, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.243 (Depositor), 0.241 (DCC)
R-Value Work:
0.208 (Depositor), 0.211 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2VPH

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of the Human Protein Tyrosine Phosphatase, Non-Receptor Type 4, Pdz Domain

Roos, A.K., Wang, J., Burgess-Brown, N., Elkins, J.M., Kavanagh, K., Pike, A.C.W., Filippakopoulos, P., Arrowsmith, C.H., Weigelt, J., Edwards, A., von Delft, F., Bountra, C., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 22.08 kDa
Atom Count: 1,496
Modeled Residue Count: 190
Deposited Residue Count: 200
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE 4	A, B	100	Homo sapiens	Mutation(s): 0 EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P29074 (Homo sapiens) Explore P29074 Go to UniProtKB: P29074
PHAROS: P29074 GTEx: ENSG00000088179
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29074
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.243 (Depositor), 0.241 (DCC)
R-Value Work: 0.208 (Depositor), 0.211 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.489	α = 90
b = 71.015	β = 90
c = 71.598	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-03-18

Deposition Author(s):

Burgess-Brown, N.

Filippakopoulos, P.

Arrowsmith, C.H.

Revision History (Full details and data files)

Version 1.0: 2008-03-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2018-01-24
Changes: Database references
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Other, 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.