3D8K

Crystal structure of a phosphatase from a toxoplasma gondii

PDB DOI: https://doi.org/10.2210/pdb3D8K/pdb

Classification: HYDROLASE
Organism(s): Toxoplasma gondii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-05-23 Released: 2008-06-17
Deposition Author(s): Damodharan, L., Burley, S.K., Swaminathan, S., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.71 Å
R-Value Free: 0.304
R-Value Work: 0.251
R-Value Observed: 0.251

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crsytal structure of a phosphatase from a toxoplasma gondii

Damodharan, L., Sauder, J.M., Burley, S.K., Swaminathan, S.

To be published.

Macromolecule Content

Total Structure Weight: 168.44 kDa
Atom Count: 10,892
Modelled Residue Count: 1,395
Deposited Residue Count: 1,508
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein phosphatase 2C	A, B, C, D	377	Toxoplasma gondii	Mutation(s): 0 Gene Names: pp2c
UniProt
Find proteins for A4GX63 (Toxoplasma gondii) Explore A4GX63 Go to UniProtKB: A4GX63
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A4GX63
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] SDF format, chain H [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] MOL2 format, chain H [auth C]	E [auth A], F [auth B], G [auth C], H [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.71 Å
R-Value Free: 0.304
R-Value Work: 0.251
R-Value Observed: 0.251
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.882	α = 90
b = 169.052	β = 104.47
c = 87.012	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CBASS	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHELXD	phasing
SOLVE	phasing
SHARP	phasing
ARP/wARP	model building

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-06-17

Deposition Author(s):

Damodharan, L.

Burley, S.K.

Swaminathan, S.

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2008-06-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-05-02
Changes: Structure summary
Version 1.3: 2018-01-24
Changes: Database references
Version 1.4: 2018-11-14
Changes: Data collection, Database references
Version 1.5: 2019-01-16
Changes: Data collection, Structure summary
Version 1.6: 2021-02-03
Changes: Database references, Derived calculations, Structure summary

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3D8K

Crystal structure of a phosphatase from a toxoplasma gondii

Crsytal structure of a phosphatase from a toxoplasma gondii

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)