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- PDB-2c7s: Crystal structure of human protein tyrosine phosphatase kappa at ... -

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Basic information

Entry
Database: PDB / ID: 2c7s
TitleCrystal structure of human protein tyrosine phosphatase kappa at 1.95A resolution
ComponentsRECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE KAPPA
KeywordsHYDROLASE / RECEPTOR TYPE TYROSINE PHOSPHATASE KAPPA / PTPRK / GLYCOPROTEIN / IMMUNOGLOBULIN DOMAIN / PROTEIN PHOSPHATASE / RECEPTOR / TRANSMEMBRANE
Function / homology
Function and homology information


transmembrane receptor protein tyrosine phosphatase activity / gamma-catenin binding / leading edge membrane / sperm head-tail coupling apparatus / focal adhesion assembly / protein localization to cell surface / protein dephosphorylation / negative regulation of cell cycle / negative regulation of keratinocyte proliferation / protein-tyrosine-phosphatase ...transmembrane receptor protein tyrosine phosphatase activity / gamma-catenin binding / leading edge membrane / sperm head-tail coupling apparatus / focal adhesion assembly / protein localization to cell surface / protein dephosphorylation / negative regulation of cell cycle / negative regulation of keratinocyte proliferation / protein-tyrosine-phosphatase / centriole / transforming growth factor beta receptor signaling pathway / protein tyrosine phosphatase activity / negative regulation of cell migration / adherens junction / cellular response to reactive oxygen species / EGFR downregulation / beta-catenin binding / neuron projection development / cell-cell junction / cellular response to UV / cell junction / cell migration / cell adhesion / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / protein kinase binding / cell surface / signal transduction / membrane / plasma membrane
Similarity search - Function
: / Receptor-type tyrosine-protein phosphatase U Fn3 domain / MAM domain signature. / : / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A ...: / Receptor-type tyrosine-protein phosphatase U Fn3 domain / MAM domain signature. / : / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / 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 / Immunoglobulin I-set / Immunoglobulin I-set 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 profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Concanavalin A-like lectin/glucanase domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Receptor-type tyrosine-protein phosphatase kappa
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsDebreczeni, J.E. / Ugochukwu, E. / Eswaran, J. / Barr, A. / Das, S. / Burgess, N. / Gileadi, O. / Longman, E. / von Delft, F. / Knapp, S. ...Debreczeni, J.E. / Ugochukwu, E. / Eswaran, J. / Barr, A. / Das, S. / Burgess, N. / Gileadi, O. / Longman, E. / von Delft, F. / Knapp, S. / Sundstron, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A.
CitationJournal: Protein Sci. / Year: 2006
Title: The crystal structure of human receptor protein tyrosine phosphatase kappa phosphatase domain 1.
Authors: Eswaran, J. / Debreczeni, J.E. / Longman, E. / Barr, A.J. / Knapp, S.
History
DepositionNov 28, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity_src_gen / struct
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _struct.title
Revision 1.4May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / pdbx_struct_special_symmetry / Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE KAPPA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1252
Polymers36,0661
Non-polymers591
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.373, 91.373, 108.415
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2066-

HOH

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Components

#1: Protein RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE KAPPA / HUMAN PROTEIN TYROSINE PHOSPHATASE KAPPA / PROTEIN-TYROSINE PHOSPHATASE KAPPA / R-PTP-KAPPA


Mass: 36065.691 Da / Num. of mol.: 1 / Fragment: RESIDUES 865-1154
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15262, protein-tyrosine-phosphatase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Compound detailsREGULATES PROCESSES INVOLVING CELL CONTACT AND ADHESION SUCH AS GROWTH CONTROL, TUMOR INVASION, AND METASTASIS
Has protein modificationY
Sequence detailsM865 CLONING ARTIFACT, PART OF HIS-TAG

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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: 3.2 Å3/Da / Density % sol: 60 %
Crystal growMethod: vapor diffusion, sitting drop
Details: SITTING DROP, 0.2M NANO3, 20% PEG3350, 10% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978978
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 19, 2005 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978978 Å / Relative weight: 1
ReflectionResolution: 1.95→52 Å / Num. obs: 32866 / % possible obs: 96.3 % / Observed criterion σ(I): 3 / Redundancy: 6.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.14
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 4.1 / % possible all: 87.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RPM

1rpm


Resolution: 1.95→69.84 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.609 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1635 5 %RANDOM
Rwork0.2 ---
obs0.201 31191 96.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2--0.59 Å20 Å2
3----1.19 Å2
Refinement stepCycle: LAST / Resolution: 1.95→69.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2299 0 4 138 2441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222371
X-RAY DIFFRACTIONr_bond_other_d0.0020.021588
X-RAY DIFFRACTIONr_angle_refined_deg1.2021.9383222
X-RAY DIFFRACTIONr_angle_other_deg0.8643.0013849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2555291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47923.628113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93115384
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4651516
X-RAY DIFFRACTIONr_chiral_restr0.0690.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022660
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02502
X-RAY DIFFRACTIONr_nbd_refined0.1890.2439
X-RAY DIFFRACTIONr_nbd_other0.1920.21619
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21135
X-RAY DIFFRACTIONr_nbtor_other0.0820.21211
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2120
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.290.227
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6241.51517
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.99722343
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.39731025
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0424.5877
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.329 85
Rwork0.276 1982
Refinement TLS params.Method: refined / Origin x: 35.426 Å / Origin y: 21.293 Å / Origin z: 34.941 Å
111213212223313233
T-0.1057 Å2-0.0105 Å20.0013 Å2--0.1199 Å20.0175 Å2---0.2326 Å2
L2.0365 °2-1.1337 °2-1.4595 °2-2.5095 °22.1641 °2--4.106 °2
S0.1985 Å °0.0793 Å °0.0318 Å °-0.2263 Å °-0.0454 Å °-0.0419 Å °-0.1569 Å °0.0409 Å °-0.1531 Å °

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