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- PDB-2g59: Crystal Structure of the Catalytic Domain of Protein Tyrosine Pho... -

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Basic information

Entry
Database: PDB / ID: 2g59
TitleCrystal Structure of the Catalytic Domain of Protein Tyrosine Phosphatase from Homo sapiens
ComponentsReceptor-type tyrosine-protein phosphatase O
KeywordsHYDROLASE / Protein Tyrosine Phosphatase / Dephosphorylation / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


slit diaphragm assembly / negative regulation of retinal ganglion cell axon guidance / regulation of glomerular filtration / Signaling by NTRK3 (TRKC) / podocyte differentiation / transmembrane receptor protein tyrosine phosphatase activity / Wnt-protein binding / glomerulus development / lamellipodium assembly / negative regulation of glomerular filtration ...slit diaphragm assembly / negative regulation of retinal ganglion cell axon guidance / regulation of glomerular filtration / Signaling by NTRK3 (TRKC) / podocyte differentiation / transmembrane receptor protein tyrosine phosphatase activity / Wnt-protein binding / glomerulus development / lamellipodium assembly / negative regulation of glomerular filtration / regulation of synapse organization / monocyte chemotaxis / phosphatase activity / lateral plasma membrane / negative regulation of cell-substrate adhesion / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / axon guidance / negative regulation of canonical Wnt signaling pathway / postsynaptic density membrane / GABA-ergic synapse / cell morphogenesis / lamellipodium / negative regulation of neuron projection development / growth cone / dendritic spine / neuron projection / apical plasma membrane / cadherin binding / axon / glutamatergic synapse / protein homodimerization activity / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Receptor-type tyrosine-protein phosphatase O / 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. ...Receptor-type tyrosine-protein phosphatase O / 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 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-like fold / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Receptor-type tyrosine-protein phosphatase O
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsKumaran, D. / Swaminathan, S. / Burley, S.K. / 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
DepositionFeb 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 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

Downloads & links

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Assembly

Deposited unit
A: Receptor-type tyrosine-protein phosphatase O
B: Receptor-type tyrosine-protein phosphatase O
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0754
Polymers69,8852
Non-polymers1902
Water4,846269
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.869, 59.723, 76.995
Angle α, β, γ (deg.)90.00, 102.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Receptor-type tyrosine-protein phosphatase O / Glomerular epithelial protein 1 / Protein tyrosine phosphatase U2 / PTPase U2 / PTP-U2


Mass: 34942.656 Da / Num. of mol.: 2 / Fragment: Protein tyrosine phosphatase, catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRO, GLEPP1, PTPU2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q16827, protein-tyrosine-phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.37 Å3/Da / Density % sol: 48.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris, 2.0 M Sodium Chloride, 5% PEG 3350, 5 mM Calcium Chloride, 10 mM Sodium Phosphate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 17, 2006 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. all: 33737 / Num. obs: 33737 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 14.8 Å2 / Rsym value: 0.098 / Net I/σ(I): 11.5
Reflection shellResolution: 2.19→2.27 Å / Redundancy: 2.5 % / Num. unique all: 3127 / Rsym value: 0.252 / % possible all: 90.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data scaling
MOLREPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2AHS

2ahs


Resolution: 2.19→31.83 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 152543.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The residues listed in remark 465 were not modeled due to lack of electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1623 4.9 %RANDOM
Rwork0.199 ---
obs0.199 32798 96.5 %-
all-32798 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.9285 Å2 / ksol: 0.366282 e/Å3
Displacement parametersBiso mean: 24.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å24.08 Å2
2---2.13 Å20 Å2
3---2.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.19→31.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4689 0 10 269 4968
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.062
X-RAY DIFFRACTIONc_scbond_it2.142
X-RAY DIFFRACTIONc_scangle_it3.072.5
LS refinement shellResolution: 2.19→2.33 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 242 4.6 %
Rwork0.216 4970 -
obs--92.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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