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- PDB-2z72: New Structure Of Cold-Active Protein Tyrosine Phosphatase At 1.1 ... -

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Basic information

Entry
Database: PDB / ID: 2z72
TitleNew Structure Of Cold-Active Protein Tyrosine Phosphatase At 1.1 Angstrom
ComponentsProtein-tyrosine-phosphatase
KeywordsHYDROLASE / COLD-ACTIVE ENZYME / PSYCHROPHILE / PROTEIN TYROSINE PHOSPHATASE / SHEWANELLA SP.
Function / homology
Function and homology information


protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / metal ion binding
Similarity search - Function
Shewanella-like phosphatase, metallophosphatase domain / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesShewanella sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.1 Å
AuthorsTsuruta, H. / Mikami, B. / Yamamoto, C. / Yamagata, H.
CitationJournal: Febs J. / Year: 2008
Title: The role of group bulkiness in the catalytic activity of psychrophile cold-active protein tyrosine phosphatase
Authors: Tsuruta, H. / Mikami, B. / Yamamoto, C. / Yamagata, H.
History
DepositionAug 10, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-tyrosine-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9803
Polymers38,8491
Non-polymers1312
Water13,908772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.565, 77.306, 81.029
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 / Cold-active protein tyrosine phosphatase


Mass: 38848.922 Da / Num. of mol.: 1 / Fragment: UNP residues 22-361
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella sp. (bacteria) / Gene: PPI / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9S427, protein-tyrosine-phosphatase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 772 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHERE ARE CONFLICTS BETWEEN SEQRES(SER) AND SEQUENCE DATABASE (GLY). THE AUTHORS BELIEVE THAT THE ...THERE ARE CONFLICTS BETWEEN SEQRES(SER) AND SEQUENCE DATABASE (GLY). THE AUTHORS BELIEVE THAT THE SEQRES IS CORRECT AND IS THE TRUE IDENTITY OF THESE RESIDUES AND IS NATURAL MUTANT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.23 Å3/Da / Density % sol: 45.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% polyethyleneglycol, 0.1M ammonium acetate, 50mM p-nitrophenylsulphate, 0.05M Tris-HCl (pH8.5), pH8.50, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.7 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 11, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.1→50 Å / Num. obs: 141407 / % possible obs: 89.2 %

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO
Starting model: PDB ENTRY 1V73

1v73


Resolution: 1.1→8 Å / Num. parameters: 32955 / Num. restraintsaints: 39804 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.1612 6225 5.2 %RANDOM
obs0.116 119401 84.7 %-
Refine analyzeNum. disordered residues: 39 / Occupancy sum hydrogen: 2670 / Occupancy sum non hydrogen: 3479.15
Refinement stepCycle: LAST / Resolution: 1.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2883 0 2 772 3657
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.031
X-RAY DIFFRACTIONs_zero_chiral_vol0.085
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.097
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.05
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.053
X-RAY DIFFRACTIONs_approx_iso_adps0.115

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