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- PDB-2fh7: Crystal structure of the phosphatase domains of human PTP SIGMA -

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Basic information

Entry
Database: PDB / ID: 2fh7
TitleCrystal structure of the phosphatase domains of human PTP SIGMA
ComponentsReceptor-type tyrosine-protein phosphatase S
KeywordsHYDROLASE / receptor protein tyrosine phosphatase / Dual domain phosphatase / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
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 / chondroitin sulfate binding / Receptor-type tyrosine-protein phosphatases / negative regulation of collateral sprouting / negative regulation of axon regeneration / negative regulation of dendritic spine development / establishment of endothelial intestinal barrier ...negative regulation of toll-like receptor 9 signaling pathway / Signaling by NTRK3 (TRKC) / trans-synaptic signaling / negative regulation of interferon-alpha production / chondroitin sulfate binding / Receptor-type tyrosine-protein phosphatases / negative regulation of collateral sprouting / negative regulation of axon regeneration / negative regulation of dendritic spine development / establishment of endothelial intestinal barrier / synaptic membrane adhesion / negative regulation of axon extension / corpus callosum development / regulation of postsynaptic density assembly / Synaptic adhesion-like molecules / negative regulation of interferon-beta production / heparan sulfate proteoglycan binding / spinal cord development / peptidyl-tyrosine dephosphorylation / phosphoprotein phosphatase activity / ECM proteoglycans / protein dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cerebellum development / hippocampus development / postsynaptic density membrane / cerebral cortex development / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / synaptic vesicle membrane / heparin binding / negative regulation of neuron projection development / presynaptic membrane / growth cone / perikaryon / axon / glutamatergic synapse / signal transduction / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
: / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Immunoglobulin domain / 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 superfamily / Protein-Tyrosine Phosphatase; Chain A / Immunoglobulin domain / 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 / 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 Å
AuthorsAlvarado, J. / Udupi, R. / Smith, D. / Koss, J. / Wasserman, S.R. / Ozyurt, S. / Atwell, S. / Powell, A. / Kearins, M.C. / Rooney, I. ...Alvarado, J. / Udupi, R. / Smith, D. / Koss, J. / Wasserman, S.R. / Ozyurt, S. / Atwell, S. / Powell, A. / Kearins, M.C. / Rooney, I. / Maletic, M. / Bain, K.T. / Freeman, J.C. / Russell, M. / Thompson, D.A. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2007
Title: Structural genomics of protein phosphatases.
Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. ...Authors: Almo, S.C. / Bonanno, J.B. / Sauder, J.M. / Emtage, S. / Dilorenzo, T.P. / Malashkevich, V. / Wasserman, S.R. / Swaminathan, S. / Eswaramoorthy, S. / Agarwal, R. / Kumaran, D. / Madegowda, M. / Ragumani, S. / Patskovsky, Y. / Alvarado, J. / Ramagopal, U.A. / Faber-Barata, J. / Chance, M.R. / Sali, A. / Fiser, A. / Zhang, Z.Y. / Lawrence, D.S. / Burley, S.K.
History
DepositionDec 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 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: Receptor-type tyrosine-protein phosphatase S


Theoretical massNumber of molelcules
Total (without water)68,7041
Polymers68,7041
Non-polymers00
Water6,503361
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.333, 94.333, 123.036
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 / Protein-tyrosine phosphatase sigma / R-PTP-sigma


Mass: 68703.688 Da / Num. of mol.: 1 / Fragment: Cytoplasmic phosphatase domains / Mutation: Residues 1365-1948
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon+ RIL / References: UniProt: Q13332, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein(10mg/ml) was crystallized in (15% PEG3350,100mM Succinic Acid)., pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.81→25.76 Å / Num. obs: 55608 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 6
Reflection shellResolution: 1.81→1.91 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.011 / Mean I/σ(I) obs: 0.6 / Num. unique all: 7637 / Rsym value: 0.0115 / % possible all: 93.3

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Phasing

Phasing MRRfactor: 0.437 / Cor.coef. Fo:Fc: 0.52
Highest resolutionLowest resolution
Rotation3 Å25.76 Å
Translation3 Å25.76 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LAR

1lar


Resolution: 2→24.67 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.802 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.195 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2103 5 %RANDOM
Rwork0.19 ---
all0.192 41832 --
obs0.19199 55608 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.698 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→24.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4648 0 0 361 5009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0224769
X-RAY DIFFRACTIONr_angle_refined_deg1.1481.9446477
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7685582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67423.417240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.78915806
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2211541
X-RAY DIFFRACTIONr_chiral_restr0.0850.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023727
X-RAY DIFFRACTIONr_nbd_refined0.1960.22174
X-RAY DIFFRACTIONr_nbtor_refined0.3030.23290
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2396
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.231
X-RAY DIFFRACTIONr_mcbond_it0.7361.52975
X-RAY DIFFRACTIONr_mcangle_it1.22824683
X-RAY DIFFRACTIONr_scbond_it1.69332068
X-RAY DIFFRACTIONr_scangle_it2.6164.51794
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 156 -
Rwork0.208 2914 -
obs-3070 99.84 %

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