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- PDB-5hde: Crystal Structure of PTPN12 Catalytic Domain -

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Basic information

Entry
Database: PDB / ID: 5hde
TitleCrystal Structure of PTPN12 Catalytic Domain
ComponentsTyrosine-protein phosphatase non-receptor type 12
KeywordsHYDROLASE / PTPN12 / PTP / protein tyrosine phosphatase / dephosphorylation
Function / homology
Function and homology information


negative regulation of platelet-derived growth factor receptor-beta signaling pathway / negative regulation of ERBB signaling pathway / regulation of epidermal growth factor receptor signaling pathway / tissue regeneration / Signaling by PDGF / Interleukin-37 signaling / podosome / phosphoprotein phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / peptidyl-tyrosine dephosphorylation ...negative regulation of platelet-derived growth factor receptor-beta signaling pathway / negative regulation of ERBB signaling pathway / regulation of epidermal growth factor receptor signaling pathway / tissue regeneration / Signaling by PDGF / Interleukin-37 signaling / podosome / phosphoprotein phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / peptidyl-tyrosine dephosphorylation / cellular response to epidermal growth factor stimulus / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cell projection / EGFR downregulation / Downregulation of ERBB2 signaling / SH3 domain binding / focal adhesion / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Protein-tyrosine phosphatase, non-receptor type-12 / : / : / 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, non-receptor type-12 / : / : / 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 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsDong, H. / Li, S. / Shi, J.
Funding support China, 2items
OrganizationGrant numberCountry
the National Natural Science Foundation of China31300601 China
the PUMC Youth Fund33320140186 China
CitationJournal: To Be Published
Title: Crystal Structure of PTPN12 Catalytic Domain
Authors: Dong, H. / Shi, J. / Li, J. / Li, S.
History
DepositionJan 5, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Oct 11, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source
Revision 1.3Nov 8, 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: Tyrosine-protein phosphatase non-receptor type 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4982
Polymers36,4031
Non-polymers951
Water6,377354
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14080 Å2
Unit cell
Length a, b, c (Å)136.010, 40.967, 75.686
Angle α, β, γ (deg.)90.00, 116.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Tyrosine-protein phosphatase non-receptor type 12 / PTP-PEST / Protein-tyrosine phosphatase G1 / PTPG1


Mass: 36403.492 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPN12 / Plasmid: pET28a / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q05209, protein-tyrosine-phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.04M potassium phosphate, 16% w/v PEG 8000, 20% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 47713 / % possible obs: 99.9 % / Redundancy: 6.1 % / Net I/σ(I): 37.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QCJ

2qcj


Resolution: 1.62→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.176 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21265 2364 5 %RANDOM
Rwork0.16421 ---
obs0.16659 45347 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.591 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å2-1.1 Å2
2--1.36 Å2-0 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 1.62→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2510 0 5 354 2869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192593
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.9513509
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3595305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28123.504137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4315465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6181522
X-RAY DIFFRACTIONr_chiral_restr0.0920.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211996
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.9911.5171208
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.4572.2721511
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5661.8271383
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined4.41615.0364459
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.68432591
X-RAY DIFFRACTIONr_sphericity_free28.796588
X-RAY DIFFRACTIONr_sphericity_bonded20.35352795
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 187 -
Rwork0.235 3242 -
obs--97.55 %
Refinement TLS params.Method: refined / Origin x: 11.0853 Å / Origin y: 0.9782 Å / Origin z: 12.9253 Å
111213212223313233
T0.0015 Å20.0025 Å20.0045 Å2-0.0428 Å2-0.0078 Å2--0.0684 Å2
L0.0784 °20.0099 °20.0467 °2-0.1183 °2-0.068 °2--0.1042 °2
S0.0015 Å °-0.0083 Å °-0.0053 Å °0.0038 Å °0.0078 Å °0.0017 Å °-0.0073 Å °-0.0272 Å °-0.0093 Å °

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