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- PDB-1pnt: CRYSTAL STRUCTURE OF BOVINE HEART PHOSPHOTYROSYL PHOSPHATASE AT 2... -

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Basic information

Entry
Database: PDB / ID: 1pnt
TitleCRYSTAL STRUCTURE OF BOVINE HEART PHOSPHOTYROSYL PHOSPHATASE AT 2.2 ANGSTROMS RESOLUTION
ComponentsACID PHOSPHATASE
KeywordsHYDROLASE
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / cytoplasm
Similarity search - Function
Protein-tyrosine phosphatase, low molecular weight, mammalian / : / Protein-tyrosine phosphatase, low molecular weight / Phosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Low molecular weight phosphotyrosine protein phosphatase
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsZhang, M. / Van Etten, R.L. / Stauffacher, C.V.
Citation
Journal: Biochemistry / Year: 1994
Title: Crystal structure of bovine heart phosphotyrosyl phosphatase at 2.2-A resolution.
Authors: Zhang, M. / Van Etten, R.L. / Stauffacher, C.V.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary X-Ray Analysis of the Low Molecular Weight Phosphotyrosyl Protein Phosphatase from Bovine Heart
Authors: Zhang, M. / Van Etten, R.L. / Lawrence, C.M. / Stauffacher, C.V.
History
DepositionAug 5, 1994Processing site: BNL
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.6Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACID PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0412
Polymers17,9461
Non-polymers951
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.300, 43.300, 41.200
Angle α, β, γ (deg.)90.00, 113.50, 90.00
Int Tables number5
Space group name H-MC121
Atom site foot note1: RESIDUES 1 - 3 ARE MODELED IN WEAKER DENSITY AND HAVE CORRESPONDINGLY HIGHER TEMPERATURE FACTORS.

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Components

#1: Protein ACID PHOSPHATASE


Mass: 17946.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P11064, acid phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
Compound detailsTHE ACTIVE SITE SEQUENCE MOTIF FOR ALL MEMBERS OF THE TYROSINE PHOSPHATASE FAMILY IS CXXXXXRS/T. ...THE ACTIVE SITE SEQUENCE MOTIF FOR ALL MEMBERS OF THE TYROSINE PHOSPHATASE FAMILY IS CXXXXXRS/T. CYS 12 TO SER 19, WHICH FORM THE LOOP BETWEEN THE BETA STRAND 1 AND ALPHA HELIX 1 OF THE FIRST BETA/ALPHA/BETA MOTIF, REPRESENT THE ACTIVE SITE LOOP IN THIS STRUCTURE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.35 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Zhang, M., (1994) J.Mol.Biol., 238, 281.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %PEG33501reservoir
250 mMTris-HCl1reservoir
350 mM1reservoirNH4Cl

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / % possible obs: 90 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.06

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→20 Å / σ(F): 0
Details: RESIDUES 1 - 3 ARE MODELED IN WEAKER DENSITY AND HAVE CORRESPONDINGLY HIGHER TEMPERATURE FACTORS.
RfactorNum. reflection
Rwork0.166 -
obs0.166 6929
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1256 0 5 0 1261
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.09
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: TNT / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d
X-RAY DIFFRACTIONt_angle_d2.09
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_improper_angle_d
X-RAY DIFFRACTIONt_mcbond_it
X-RAY DIFFRACTIONt_scbond_it
X-RAY DIFFRACTIONt_mcangle_it
X-RAY DIFFRACTIONt_scangle_it

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