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- PDB-2zbm: Crystal Structure of I115M Mutant Cold-Active Protein Tyrosine Ph... -

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Basic information

Entry
Database: PDB / ID: 2zbm
TitleCrystal Structure of I115M Mutant Cold-Active Protein Tyrosine Phosphatase
ComponentsProtein-tyrosine-phosphatase
KeywordsHYDROLASE / HYDRASE / PROTEIN-TYROSINE-PHOSPHATASE / METALLOPHOSPHOESTERASE
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 PHASING / Resolution: 1.5 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
DepositionOct 24, 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 10, 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 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Protein-tyrosine-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2823
Polymers38,1511
Non-polymers1312
Water8,089449
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.172, 77.559, 80.331
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


Mass: 38151.254 Da / Num. of mol.: 1 / Fragment: Residues UNP 22-355 / Mutation: I115M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella sp. (bacteria) / Gene: PPI / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / Strain (production host): AD494(DE3) / 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.: 449 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% POLYETHYLENEGLYCOL 4000, 0.1M AMMONIUM ACETATE, 0.05M TRIS-HCL (PH 8.5), VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: May 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→15 Å / Num. all: 51223 / Num. obs: 54976 / % possible obs: 97.7 % / Redundancy: 9.1 % / Rsym value: 0.126
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 6.9 % / Rsym value: 0.24 / % possible all: 84.7

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.5→10 Å / Num. parameters: 28732 / Num. restraintsaints: 35139 / 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
Rfree0.1973 2705 5.3 %RANDOM
all0.1263 51223 --
obs0.1216 53928 93.7 %-
Refine analyzeNum. disordered residues: 19 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3103
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2739 0 2 449 3190
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.012
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0284
X-RAY DIFFRACTIONs_zero_chiral_vol0.05
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.063
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.015
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.055
X-RAY DIFFRACTIONs_approx_iso_adps0.097

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