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- PDB-1c0e: Active Site S19A Mutant of Bovine Heart Phosphotyrosyl Phosphatase -

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Basic information

Entry
Database: PDB / ID: 1c0e
TitleActive Site S19A Mutant of Bovine Heart Phosphotyrosyl Phosphatase
ComponentsPROTEIN (TYROSINE PHOSPHATASE (ORTHOPHOSPHORIC MONOESTER PHOSPHOHYDROLASE))
KeywordsHYDROLASE / TYROSINE PHOSPHATASE / PHOSPHATASE DIMER
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / 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
AuthorsTabernero, L. / Evans, B.N. / Tishmack, P.A. / Van Etten, R.L. / Stauffacher, C.V.
Citation
Journal: Biochemistry / Year: 1999
Title: The structure of the bovine protein tyrosine phosphatase dimer reveals a potential self-regulation mechanism.
Authors: Tabernero, L. / Evans, B.N. / Tishmack, P.A. / Van Etten, R.L. / Stauffacher, C.V.
#1: Journal: Biochemistry / Year: 1994
Title: Structure of Bovine Heart Phosphotyrosyl Phosphatase at 2.2 Angstroms Resolution
Authors: Zhang, M. / Van Etten, R.L. / Stauffacher, C.V.
History
DepositionJul 15, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (TYROSINE PHOSPHATASE (ORTHOPHOSPHORIC MONOESTER PHOSPHOHYDROLASE))
B: PROTEIN (TYROSINE PHOSPHATASE (ORTHOPHOSPHORIC MONOESTER PHOSPHOHYDROLASE))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0514
Polymers35,8612
Non-polymers1902
Water1,76598
1
A: PROTEIN (TYROSINE PHOSPHATASE (ORTHOPHOSPHORIC MONOESTER PHOSPHOHYDROLASE))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0252
Polymers17,9301
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (TYROSINE PHOSPHATASE (ORTHOPHOSPHORIC MONOESTER PHOSPHOHYDROLASE))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0252
Polymers17,9301
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.320, 55.470, 131.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN (TYROSINE PHOSPHATASE (ORTHOPHOSPHORIC MONOESTER PHOSPHOHYDROLASE))


Mass: 17930.326 Da / Num. of mol.: 2 / Mutation: S19A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Organ: HEART / Production host: Escherichia coli (E. coli) / References: UniProt: P11064, acid phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.13 %
Crystal growpH: 7 / Details: PEG 4000, TRIS BUFFER, pH 7.00
Crystal grow
*PLUS
pH: 7 / Method: unknown / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein11
230 %PEG400012
30.1 MTris12

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 15, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 15625 / % possible obs: 93.4 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 15
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 1 % / Rmerge(I) obs: 0.306 / % possible all: 67.7
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 30 Å / Observed criterion σ(I): 0 / Redundancy: 3 %
Reflection shell
*PLUS
Redundancy: 1 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.2→20 Å / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.244 688 RANDOM
Rwork0.191 --
obs0.191 13757 -
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2464 0 10 98 2572
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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