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- PDB-4bpc: Structure of the Catalytic Domain of Protein Tyrosine Phosphatase... -

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Basic information

Entry
Database: PDB / ID: 4bpc
TitleStructure of the Catalytic Domain of Protein Tyrosine Phosphatase Sigma in the Sulfenic Acid Form
ComponentsRECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE S
KeywordsHYDROLASE / PROTEOGLYCAN / REDOX REGULATION
Function / homology
Function and homology information


negative regulation of toll-like receptor 9 signaling pathway / Signaling by NTRK3 (TRKC) / trans-synaptic signaling / negative regulation of interferon-alpha production / Receptor-type tyrosine-protein phosphatases / chondroitin sulfate binding / negative regulation of collateral sprouting / negative regulation of axon regeneration / establishment of endothelial intestinal barrier / negative regulation of dendritic spine development ...negative regulation of toll-like receptor 9 signaling pathway / Signaling by NTRK3 (TRKC) / trans-synaptic signaling / negative regulation of interferon-alpha production / Receptor-type tyrosine-protein phosphatases / chondroitin sulfate binding / negative regulation of collateral sprouting / negative regulation of axon regeneration / establishment of endothelial intestinal barrier / negative regulation of dendritic spine development / regulation of postsynaptic density assembly / synaptic membrane adhesion / negative regulation of axon extension / Synaptic adhesion-like molecules / corpus callosum development / heparan sulfate proteoglycan binding / negative regulation of interferon-beta production / spinal cord development / phosphoprotein phosphatase activity / peptidyl-tyrosine dephosphorylation / ECM proteoglycans / cerebellum development / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / hippocampus development / postsynaptic density membrane / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / synaptic vesicle membrane / cerebral cortex development / negative regulation of neuron projection development / presynaptic membrane / heparin binding / growth cone / perikaryon / axon / glutamatergic synapse / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
Protein tyrosine phosphatase superfamily / Immunoglobulin domain / Protein-Tyrosine Phosphatase; Chain A / Immunoglobulin I-set / Immunoglobulin I-set domain / 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 superfamily / Immunoglobulin domain / Protein-Tyrosine Phosphatase; Chain A / Immunoglobulin I-set / Immunoglobulin I-set domain / 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 / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase S
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJeon, T.J. / Chien, P.N. / Chun, H.J. / Ryu, S.E.
CitationJournal: Mol.Cells / Year: 2013
Title: Structure of the Catalytic Domain of Protein Tyrosine Phosphatase Sigma in the Sulfenic Acid Form
Authors: Jeon, T.J. / Chien, P.N. / Chun, H.J. / Ryu, S.E.
History
DepositionMay 24, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Sep 23, 2015Group: Data collection
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE S


Theoretical massNumber of molelcules
Total (without water)66,9331
Polymers66,9331
Non-polymers00
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.672, 94.672, 123.423
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 RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE S / R-PTP-S / RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE SIGMA /


Mass: 66932.555 Da / Num. of mol.: 1
Fragment: CYTOPLASMIC PHOSPHATASE DOMAINS, RESIDUES 1367-1948
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q13332, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE BASED ON NCBI: NM_002850.2.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.96 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.8M SUCCINIC ACID, PH 7.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 30, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 36574 / % possible obs: 98.2 % / Observed criterion σ(I): 7.9 / Redundancy: 5.7 % / Rmerge(I) obs: 0.06
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 7.4 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FH7

2fh7


Resolution: 2.1→37.56 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.783 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22198 1781 5 %RANDOM
Rwork0.17827 ---
obs0.18042 34043 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.252 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.02 Å20 Å2
2--0.02 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.1→37.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4587 0 0 181 4768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194707
X-RAY DIFFRACTIONr_bond_other_d0.0050.024391
X-RAY DIFFRACTIONr_angle_refined_deg1.7361.9426383
X-RAY DIFFRACTIONr_angle_other_deg0.908310075
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5135567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74323.568241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38515787
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2661539
X-RAY DIFFRACTIONr_chiral_restr0.1090.2677
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215387
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021158
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 115 -
Rwork0.267 2430 -
obs--95.68 %

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