1LYV | pdb_00001lyv

High-resolution structure of the catalytically inactive yersinia tyrosine phosphatase C403A mutant in complex with phosphate.

PDB DOI: https://doi.org/10.2210/pdb1LYV/pdb

Classification: HYDROLASE
Organism(s): Yersinia enterocolitica
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2002-06-08 Released: 2002-07-03
Deposition Author(s): Evdokimov, A.G., Waugh, D.S., Routzahn, K., Tropea, J., Cherry, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.36 Å
R-Value Free:
0.190 (Depositor), 0.190 (DCC)
R-Value Work:
0.132 (DCC)
R-Value Observed:
0.129 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1LYV

This is version 1.5 of the entry. See complete history.

Literature

High-resolution structure of the catalytically inactive yersinia tyrosine phosphatase C403A mutant in complex with phosphate.

Evdokimov, A.G., Waugh, D.S., Routzahn, K., Tropea, J., Cherry, S.

To be published.

Macromolecule Content

Total Structure Weight: 33.67 kDa
Atom Count: 2,542
Modeled Residue Count: 283
Deposited Residue Count: 306
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN-TYROSINE PHOSPHATASE YOPH	A	306	Yersinia enterocolitica	Mutation(s): 3 Gene Names: YopH EC: 3.1.3.48
UniProt
Find proteins for P15273 (Yersinia enterocolitica) Explore P15273 Go to UniProtKB: P15273
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15273
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.36 Å
R-Value Free: 0.190 (Depositor), 0.190 (DCC)
R-Value Work: 0.132 (DCC)
R-Value Observed: 0.129 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.456	α = 90
b = 49.331	β = 90
c = 97.537	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2002-07-03

Deposition Author(s):

Evdokimov, A.G.

Revision History (Full details and data files)

Version 1.0: 2002-07-03
Type: Initial release
Version 1.1: 2008-04-28
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2021-10-27
Changes: Database references, Derived calculations
Version 1.5: 2024-02-14
Changes: Data collection, 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.