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- PDB-2gp0: HePTP Catalytic Domain (residues 44-339), S225D mutant -

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Basic information

Entry
Database: PDB / ID: 2gp0
TitleHePTP Catalytic Domain (residues 44-339), S225D mutant
ComponentsTyrosine-protein phosphatase non-receptor type 7
KeywordsHYDROLASE / HePTP / Human Hemapoietic Tyrosine Phosphatase Catalytic Domain / PTPN7
Function / homology
Function and homology information


Interleukin-37 signaling / non-membrane spanning protein tyrosine phosphatase activity / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasmic side of plasma membrane / mitotic spindle / Negative regulation of MAPK pathway / microtubule cytoskeleton / MAPK cascade ...Interleukin-37 signaling / non-membrane spanning protein tyrosine phosphatase activity / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasmic side of plasma membrane / mitotic spindle / Negative regulation of MAPK pathway / microtubule cytoskeleton / MAPK cascade / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Protein-tyrosine phosphatase, KIM-containing / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / 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, KIM-containing / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / 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
PHOSPHATE ION / Tyrosine-protein phosphatase non-receptor type 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.05 Å
AuthorsPage, R.
CitationJournal: To be Published
Title: HePTP Catalytic Domain (residues 44-339), S225D mutant
Authors: Page, R. / Mustelin, T.
History
DepositionApr 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 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 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein phosphatase non-receptor type 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5513
Polymers35,3641
Non-polymers1872
Water5,350297
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.520, 127.520, 60.133
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 7 / Protein-tyrosine phosphatase LC-PTP / Hematopoietic protein-tyrosine phosphatase / HEPTP


Mass: 35364.000 Da / Num. of mol.: 1 / Fragment: Catalytic Domain (residues 65-360) / Mutation: S225D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN7 / Production host: Escherichia coli (E. coli) / References: UniProt: P35236, protein-tyrosine-phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 4.23 Å3/Da / Density % sol: 70.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: K/Na Phosphate, Ammonium Acetate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 1, 2005
RadiationMonochromator: Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 33843 / Num. obs: 33843 / % possible obs: 96.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rmerge(I) obs: 0.089 / Χ2: 1.118 / Net I/σ(I): 9.9
Reflection shellResolution: 2.05→2.12 Å / % possible obs: 82.5 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.456 / Num. unique obs: 2882 / Χ2: 0.958 / % possible all: 82.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
CrystalClear(MSC/RIGAKU)data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB Entry 1ZC0

1zc0


Resolution: 2.05→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.278 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1689 5 %RANDOM
Rwork0.178 ---
all0.179 33803 --
obs0.179 33803 96.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.403 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.03 Å20 Å2
2--0.07 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2267 0 11 297 2575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222415
X-RAY DIFFRACTIONr_angle_refined_deg1.5881.963296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7375301
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15123.866119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48415401
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6251519
X-RAY DIFFRACTIONr_chiral_restr0.0990.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021875
X-RAY DIFFRACTIONr_nbd_refined0.20.21094
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21619
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2242
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.229
X-RAY DIFFRACTIONr_mcbond_it1.0891.51516
X-RAY DIFFRACTIONr_mcangle_it1.74522391
X-RAY DIFFRACTIONr_scbond_it2.37731028
X-RAY DIFFRACTIONr_scangle_it3.6464.5897
LS refinement shellResolution: 2.05→2.104 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 101 -
Rwork0.275 1958 -
obs-2059 80.52 %

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