[English] 日本語
Yorodumi
- PDB-2gjt: Crystal structure of the human receptor phosphatase PTPRO -

+
Open data


ID or keywords:

Loading...

-
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 / 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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more