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- PDB-5z5b: Crystal structure of Tk-PTP in the G95A mutant form -

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Basic information

Entry
Database: PDB / ID: 5z5b
TitleCrystal structure of Tk-PTP in the G95A mutant form
ComponentsProtein-tyrosine phosphatase
KeywordsHYDROLASE / tyrosine phosphatase
Function / homology
Function and homology information


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 profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / PTP type protein phosphatase domain profile. / Tyrosine-specific protein phosphatase, PTPase domain ...: / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / 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
FORMIC ACID / Protein-tyrosine phosphatase
Similarity search - Component
Biological speciesThermococcus kodakarensis KOD1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
B: Protein-tyrosine phosphatase
C: Protein-tyrosine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7648
Polymers55,5553
Non-polymers2095
Water00
1
A: Protein-tyrosine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6003
Polymers18,5181
Non-polymers812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-5 kcal/mol
Surface area7720 Å2
MethodPISA
2
B: Protein-tyrosine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6003
Polymers18,5181
Non-polymers812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area7850 Å2
MethodPISA
3
C: Protein-tyrosine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5642
Polymers18,5181
Non-polymers461
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.796, 154.796, 75.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Protein-tyrosine phosphatase


Mass: 18518.312 Da / Num. of mol.: 3 / Mutation: G95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis KOD1 (archaea)
Strain: KOD1 / Gene: Tk-ptp, TK0241 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8X270
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2

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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: 3.13 Å3/Da / Density % sol: 60.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Bis-Tris (pH 6.25) and 0.8M magnesium formate dehydrate

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.298→77.4 Å / Num. obs: 28515 / % possible obs: 95.2 % / Redundancy: 4.3 % / Net I/σ(I): 27
Reflection shellResolution: 2.298→2.34 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Z5A

5z5a


Resolution: 2.3→77.4 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.881 / SU B: 8.346 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.31 / ESU R Free: 0.243 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26459 1374 5.1 %RANDOM
Rwork0.21923 ---
obs0.2216 25754 90.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.539 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0.08 Å20 Å2
2---0.16 Å20 Å2
3---0.53 Å2
Refinement stepCycle: 1 / Resolution: 2.3→77.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3707 0 11 0 3718
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0193782
X-RAY DIFFRACTIONr_bond_other_d0.0020.023687
X-RAY DIFFRACTIONr_angle_refined_deg1.8681.9795096
X-RAY DIFFRACTIONr_angle_other_deg1.07738487
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3845458
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9922.67176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.44915702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1651544
X-RAY DIFFRACTIONr_chiral_restr0.10.2559
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214144
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02800
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.853.5751842
X-RAY DIFFRACTIONr_mcbond_other2.853.5751843
X-RAY DIFFRACTIONr_mcangle_it4.4455.3542296
X-RAY DIFFRACTIONr_mcangle_other4.4445.3562297
X-RAY DIFFRACTIONr_scbond_it3.2673.9821940
X-RAY DIFFRACTIONr_scbond_other3.2673.9881935
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.225.8172801
X-RAY DIFFRACTIONr_long_range_B_refined6.95240.7374078
X-RAY DIFFRACTIONr_long_range_B_other6.95140.7534079
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.298→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 60 -
Rwork0.286 1363 -
obs--64.27 %

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