[English] 日本語
Yorodumi
- PDB-3qcb: Human receptor protein tyrosine phosphatase gamma, domain 1, apo -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qcb
TitleHuman receptor protein tyrosine phosphatase gamma, domain 1, apo
ComponentsReceptor-type tyrosine-protein phosphatase gamma
KeywordsHYDROLASE / TYROSINE RECEPTOR PHOSPHATASE / TWISTED MIXED BETA-SHEETS FLANKED BY {ALPHA}-HELICES / APO
Function / homology
Function and homology information


transmembrane receptor protein tyrosine phosphatase activity / negative regulation of epithelial cell migration / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cell surface receptor protein tyrosine kinase signaling pathway / neuron projection development / negative regulation of neuron projection development / signal transduction / extracellular exosome / identical protein binding / plasma membrane
Similarity search - Function
Receptor-type tyrosine-protein phosphatase, carbonic anhydrase domain / : / 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 ...Receptor-type tyrosine-protein phosphatase, carbonic anhydrase domain / : / 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 / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / 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 gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSheriff, S.
Citation
Journal: J.Med.Chem. / Year: 2011
Title: Small molecule receptor protein tyrosine phosphatase [gamma](RPTP[gamma]) ligands that inhibit phosphatase activity via perturbation of the tryptophan-proline-aspartate (WPD) loop
Authors: Sheriff, S. / Beno, B.R. / Zhai, W. / Kostich, W.A. / McDonnell, P.A. / Kish, K. / Goldfarb, V. / Gao, M. / Kiefer, S.E. / Yanchunas, J. / Huang, Y. / Shi, S. / Zhu, S. / Dzierba, C. / ...Authors: Sheriff, S. / Beno, B.R. / Zhai, W. / Kostich, W.A. / McDonnell, P.A. / Kish, K. / Goldfarb, V. / Gao, M. / Kiefer, S.E. / Yanchunas, J. / Huang, Y. / Shi, S. / Zhu, S. / Dzierba, C. / Bronson, J. / Macor, J.E. / Appiah, K.K. / Westphal, R.S. / O'Connell, J. / Gerritz, S.W.
#1: Journal: To be Published
Title: Cloning, purification, crystallization and preliminary X-ray analysis of the catalytic domain of human receptor-like protein Tyrosine Phosphatase g in three different crystal forms
Authors: Kish, K. / McDonnell, P.A. / Goldfarb, V. / Gao, M. / Metzler, W.J. / Langley, D.R. / Bryson, J.W. / Kiefer, S.E. / Kostich, W.A. / Carpenter, B. / Westphal, R.S. / Sheriff, S.
History
DepositionJan 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 gamma
B: Receptor-type tyrosine-protein phosphatase gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9928
Polymers71,4152
Non-polymers5766
Water3,135174
1
A: Receptor-type tyrosine-protein phosphatase gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0925
Polymers35,7081
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Receptor-type tyrosine-protein phosphatase gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9003
Polymers35,7081
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.900, 79.500, 123.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Receptor-type tyrosine-protein phosphatase gamma / Protein-tyrosine phosphatase gamma / R-PTP-gamma


Mass: 35707.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PTPG, PTPRG / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P23470, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.58 Å3/Da / Density % sol: 52.37 %
Crystal growTemperature: 277 K / pH: 6.5 / Details: pH 6.5, vapor diffusion, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Nov 15, 2005 / Details: MICROMAX CONFOCAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 43827 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 18.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 3.2 / % possible all: 99

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.1data extraction
HKL-2000(DENZO)data reduction
HKL-2000(SCALEPACK)data scaling
AMoREphasing
CNX2005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RPM WITH LOOPS EXCISED AND NON- IDENTICAL SIDE CHAINS SHORN.

1rpm


Resolution: 2.1→23.66 Å / Rfactor Rfree error: 0.012 / Occupancy max: 1 / Occupancy min: 0 / Data cutoff high absF: 2223360 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.304 644 1.5 %RANDOM
Rwork0.254 ---
obs0.255 43143 98.3 %-
all-43143 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.64 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 28.3 Å2
Baniso -1Baniso -2Baniso -3
1--4.49 Å20 Å20 Å2
2--4.64 Å20 Å2
3----0.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.1→23.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4539 0 30 174 4743
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.57
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it1.962
X-RAY DIFFRACTIONc_scbond_it2.12
X-RAY DIFFRACTIONc_scangle_it2.982.5
LS refinement shellResolution: 2.1→2.2 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.315 92 1.7 %
Rwork0.261 5220 -
obs--98.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4TMN.PARTMN.TOP

+
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