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- PDB-2gjt: Crystal structure of the human receptor phosphatase PTPRO -

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Basic information

Entry
Database: PDB / ID: 2gjt
TitleCrystal structure of the human receptor phosphatase PTPRO
ComponentsReceptor-type tyrosine-protein phosphatase PTPRO
KeywordsHYDROLASE / Tyrosine phosphatase / PTPRO / GLEPP1 / PTPU2 / Structural Genomics / Structural Genomics Consortium / SGC
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 / phosphatase activity / monocyte chemotaxis / peptidyl-tyrosine dephosphorylation / negative regulation of cell-substrate adhesion / lateral plasma membrane / protein dephosphorylation / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / axon guidance / GABA-ergic synapse / negative regulation of canonical Wnt signaling pathway / postsynaptic density membrane / cell morphogenesis / lamellipodium / negative regulation of neuron projection development / growth cone / dendritic spine / neuron projection / cadherin binding / apical plasma membrane / 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 / Tyrosine specific protein phosphatases domain profile. / 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
Receptor-type tyrosine-protein phosphatase O
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsBarr, A. / Ugochukwu, E. / Eswaran, J. / Das, S. / Niesen, F. / Savitsky, P. / Turnbull, A. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. ...Barr, A. / Ugochukwu, E. / Eswaran, J. / Das, S. / Niesen, F. / Savitsky, P. / Turnbull, A. / Sundstrom, M. / Arrowsmith, C. / Edwards, A. / Weigelt, J. / von Delft, F. / Papagrigoriou, E. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: Large-scale structural analysis of the classical human protein tyrosine phosphatome.
Authors: Barr, A.J. / Ugochukwu, E. / Lee, W.H. / King, O.N. / Filippakopoulos, P. / Alfano, I. / Savitsky, P. / Burgess-Brown, N.A. / Muller, S. / Knapp, S.
History
DepositionMar 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Mar 21, 2012Group: Database references
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,4818
Polymers69,2692
Non-polymers2136
Water3,783210
1
A: Receptor-type tyrosine-protein phosphatase PTPRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8126
Polymers34,6341
Non-polymers1775
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Receptor-type tyrosine-protein phosphatase PTPRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6702
Polymers34,6341
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-75 kcal/mol
Surface area25480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.060, 131.060, 77.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 34634.383 Da / Num. of mol.: 2 / Fragment: residues 916-1208
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPRO, GLEPP1, PTPU2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q16827, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.77 Å3/Da / Density % sol: 55.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Isopropanol, PEG4K, pH 8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.95 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 24, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.15→42.91 Å / Num. all: 41322 / Num. obs: 41322 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.15→2.25 Å / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AHS

2ahs


Resolution: 2.15→42.91 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.935 / SU B: 10.179 / SU ML: 0.134 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23366 2076 5 %RANDOM
Rwork0.17924 ---
all0.18192 39238 --
obs0.18192 39238 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.05 Å20 Å2
2---0.09 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.15→42.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4590 0 6 210 4806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224725
X-RAY DIFFRACTIONr_bond_other_d0.0020.023164
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.9336408
X-RAY DIFFRACTIONr_angle_other_deg0.99537675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8615572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84223.966237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76215784
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8231529
X-RAY DIFFRACTIONr_chiral_restr0.0990.2686
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025282
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02997
X-RAY DIFFRACTIONr_nbd_refined0.2160.2941
X-RAY DIFFRACTIONr_nbd_other0.1950.23218
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22281
X-RAY DIFFRACTIONr_nbtor_other0.0870.22365
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2184
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1230.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2190.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.27
X-RAY DIFFRACTIONr_mcbond_it6.37453017
X-RAY DIFFRACTIONr_mcbond_other2.53651141
X-RAY DIFFRACTIONr_mcangle_it7.29274635
X-RAY DIFFRACTIONr_scbond_it9.67592050
X-RAY DIFFRACTIONr_scangle_it11.126111770
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 134 -
Rwork0.215 2884 -
obs--99.02 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.16570.3538-0.45592.016-0.23582.1328-0.01940.1550.09060.03450.02590.20140.06320.0109-0.0064-0.2570.0561-0.0533-0.1355-0.0348-0.1022-13.3798-38.8191-5.4027
22.84890.07230.60382.2168-0.92333.440.0254-0.4281-0.16450.43310.14110.0890.0553-0.4599-0.1666-0.08430.0522-0.0240.00170.0486-0.11311.951-49.355621.6184
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA914 - 12081 - 295
2X-RAY DIFFRACTION2BB914 - 12011 - 288

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