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- PDB-5z59: Crystal structure of Tk-PTP in the inactive form -

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Basic information

Entry
Database: PDB / ID: 5z59
TitleCrystal structure of Tk-PTP in the inactive form
ComponentsProtein-tyrosine phosphatase
KeywordsHYDROLASE / tyrosine phosphatase
Function / homology
Function and homology information


protein tyrosine/serine/threonine phosphatase activity / dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasm
Similarity search - Function
Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / PTP type protein phosphatase domain profile. / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic ...Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / PTP type protein phosphatase domain profile. / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.703 Å
AuthorsKu, B. / Yun, H.Y. / Kim, S.J.
CitationJournal: PLoS ONE / Year: 2018
Title: Structural study reveals the temperature-dependent conformational flexibility of Tk-PTP, a protein tyrosine phosphatase from Thermococcus kodakaraensis KOD1
Authors: Yun, H.Y. / Lee, J. / Kim, H. / Ryu, H. / Shin, H.C. / Oh, B.H. / Ku, B. / Kim, S.J.
History
DepositionJan 17, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-tyrosine phosphatase


Theoretical massNumber of molelcules
Total (without water)16,9781
Polymers16,9781
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7310 Å2
Unit cell
Length a, b, c (Å)29.473, 50.638, 78.538
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: 16977.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: Tk-ptp, TK0241 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8X270
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 1.73 Å3/Da / Density % sol: 28.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium citrate (pH 5.4), 8%(w/v) polyethylene glycol 10000, 14%(v/v) dioxane

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 13111 / % possible obs: 97.2 % / Redundancy: 5.4 % / Net I/σ(I): 46
Reflection shellResolution: 1.7→1.73 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I6I

2i6i


Resolution: 1.703→31.032 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.56 / Phase error: 24
RfactorNum. reflection% reflection
Rfree0.2272 1308 10 %
Rwork0.1856 --
obs0.1899 13084 97.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.703→31.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1183 0 0 106 1289
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071206
X-RAY DIFFRACTIONf_angle_d0.9051628
X-RAY DIFFRACTIONf_dihedral_angle_d18.005737
X-RAY DIFFRACTIONf_chiral_restr0.056176
X-RAY DIFFRACTIONf_plane_restr0.006212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7031-1.77130.3241360.25591220X-RAY DIFFRACTION93
1.7713-1.85190.2771400.24051266X-RAY DIFFRACTION95
1.8519-1.94950.28341430.21991283X-RAY DIFFRACTION97
1.9495-2.07160.29391400.1991272X-RAY DIFFRACTION97
2.0716-2.23150.22341450.18521308X-RAY DIFFRACTION98
2.2315-2.4560.27161480.19521332X-RAY DIFFRACTION99
2.456-2.81120.23231480.2021323X-RAY DIFFRACTION99
2.8112-3.5410.2361500.17361353X-RAY DIFFRACTION99
3.541-31.03670.17051580.1591419X-RAY DIFFRACTION97

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