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- PDB-1phr: THE CRYSTAL STRUCTURE OF A LOW MOLECULAR PHOSPHOTYROSINE PROTEIN ... -

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Basic information

Entry
Database: PDB / ID: 1phr
TitleTHE CRYSTAL STRUCTURE OF A LOW MOLECULAR PHOSPHOTYROSINE PROTEIN PHOSPHATASE
ComponentsLOW MOLECULAR WEIGHT PHOSPHOTYROSINE PROTEIN PHOSPHATASE
KeywordsPHOSPHOTYROSINE PROTEIN PHOSPHATASE
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
Low molecular weight phosphotyrosine protein phosphatase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsSu, X.-D. / Taddei, N. / Stefani, M. / Ramponi, G. / Nordlund, P.
Citation
Journal: Nature / Year: 1994
Title: The crystal structure of a low-molecular-weight phosphotyrosine protein phosphatase.
Authors: Su, X.D. / Taddei, N. / Stefani, M. / Ramponi, G. / Nordlund, P.
#1: Journal: FEBS Lett. / Year: 1994
Title: Crystallisation of a Low Molecular Weight Phosphotyrosine Protein Phosphatase from Bovine Liver
Authors: Su, X.-D. / Agango, E.G. / Taddei, N. / Bucciantini, M. / Stefani, M. / Ramponi, G. / Nordlund, P.
History
DepositionJul 5, 1994Processing site: BNL
Revision 1.0Jul 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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

Downloads & links

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Assembly

Deposited unit
A: LOW MOLECULAR WEIGHT PHOSPHOTYROSINE PROTEIN PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0422
Polymers17,9461
Non-polymers961
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.300, 62.200, 62.700
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 LOW MOLECULAR WEIGHT PHOSPHOTYROSINE PROTEIN PHOSPHATASE


Mass: 17946.326 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P11064, protein-tyrosine-phosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.09 %
Crystal grow
*PLUS
pH: 5.5 / Method: unknown / Details: used as seeds
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 %ammonium sulfate11
210 mMDTT11
3100 mMacetate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 18781 / % possible obs: 90 %
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 9896 / Rmerge(I) obs: 0.064

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.1→6 Å / σ(F): 2
RfactorNum. reflection
Rfree0.232 -
Rwork0.167 -
obs0.167 9896
Displacement parametersBiso mean: 20.4 Å2
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1233 0 5 70 1308
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg2.7
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
Refinement
*PLUS
Rfactor obs: 0.156 / Rfactor Rfree: 0.208 / Rfactor Rwork: 0.156
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg2.6

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