[English] 日本語
Yorodumi
- PDB-1dg9: CRYSTAL STRUCTURE OF BOVINE LOW MOLECULAR WEIGHT PTPASE COMPLEXED... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1dg9
TitleCRYSTAL STRUCTURE OF BOVINE LOW MOLECULAR WEIGHT PTPASE COMPLEXED WITH HEPES
ComponentsTYROSINE PHOSPHATASEProtein tyrosine phosphatase
KeywordsHYDROLASE / PTPASE / HEPES COMPLEX
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / cytoplasm
Similarity search - Function
Protein-tyrosine phosphatase, low molecular weight, mammalian / Protein-tyrosine phosphatase, low molecular weight / Phosphotyrosine protein phosphatase I / Phosphotyrosine protein phosphatase I superfamily / Low molecular weight phosphotyrosine protein phosphatase / Low molecular weight phosphatase family / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Low molecular weight phosphotyrosine protein phosphatase
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsZhang, M. / Zhou, M. / Van Etten, R.L. / Stauffacher, C.V.
CitationJournal: Biochemistry / Year: 1997
Title: Crystal structure of bovine low molecular weight phosphotyrosyl phosphatase complexed with the transition state analog vanadate.
Authors: Zhang, M. / Zhou, M. / Van Etten, R.L. / Stauffacher, C.V.
History
DepositionNov 23, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: TYROSINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1852
Polymers17,9461
Non-polymers2381
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.300, 43.400, 41.200
Angle α, β, γ (deg.)90.00, 113.40, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein TYROSINE PHOSPHATASE / Protein tyrosine phosphatase


Mass: 17946.326 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Organ: HEART / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: UniProt: P11064, protein-tyrosine-phosphatase
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growMethod: vapor diffusion / pH: 7.5
Details: 20% PEG4k, 10% 2-propanol, 100mM HEPES, pH 7.5, VAPOR DIFFUSION
Temp details: RT
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein11
22-5 mMinorganic phosphate11
320 %PEG400012
410 %2-propanol12
5100 mMHEPES12

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.9 Å / Num. obs: 71205 / % possible obs: 98.3 % / Rmerge(I) obs: 0.065
Reflection shellHighest resolution: 1.9 Å
Reflection
*PLUS
Num. obs: 12122 / Num. measured all: 71205

-
Processing

Software
NameClassification
SCALEPACKdata scaling
AMoREphasing
TNTrefinement
RefinementResolution: 1.9→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: engh & huber /
RfactorNum. reflection
obs0.179 11869
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1256 0 15 0 1271
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg2.34
Software
*PLUS
Name: TNT / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg14.2

+
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