[English] 日本語
Yorodumi
- PDB-2i42: Crystal structure of Yersinia protein tyrosine phosphatase comple... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2i42
TitleCrystal structure of Yersinia protein tyrosine phosphatase complexed with vanadate, a transition state analogue
ComponentsTyrosine-protein phosphatase
KeywordsHYDROLASE / Yersinia PTPase / vanadate / transition state analogue
Function / homology
Function and homology information


dephosphorylation / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / extracellular region
Similarity search - Function
Protein-tyrosine phosphatase, YopH, N-terminal / Protein-tyrosine phosphatase, YopH, N-terminal domain superfamily / YopH, N-terminal / Type III secreted modular tyrosine phosphatase, SptP/YopH / 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, YopH, N-terminal / Protein-tyrosine phosphatase, YopH, N-terminal domain superfamily / YopH, N-terminal / Type III secreted modular tyrosine phosphatase, SptP/YopH / 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 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
VANADATE ION / Tyrosine-protein phosphatase YopH
Similarity search - Component
Biological speciesYersinia enterocolitica (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsVijayalakshmi, J. / Saper, M.A.
Citation
Journal: To be Published
Title: Crystal structure of Yersinia protein tyrosine phosphatase complexed with vanadate, a transition state analogue
Authors: Vijayalakshmi, J. / Saper, M.A.
#1: Journal: PROC.NATL.ACAD.SCI.USA / Year: 1995
Title: Visualization of intermediate and transition-state structures in protein tyrosine phosphatase catalysis.
Authors: Denu, J.M. / Lohse, D.L. / Vijayalakshmi, J. / Saper, M.A. / Dixon, J.E.
#2: Journal: PROTEIN SCI. / Year: 1995
Title: A ligand-induced conformational change in the Yersinia protein tyrosine phosphatase.
Authors: Schubert, H.L. / Fauman, E.B. / Stuckey, J.A. / Dixon, J.E. / Saper, M.A.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Dissecting the catalytic mechanism of protein tyrosine phosphatases.
Authors: Zhang, Z.-Y. / Wang, Y. / Dixon, J.E.
History
DepositionAug 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 29, 2013Group: Non-polymer description
Revision 1.4Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.5Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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
Remark 600HETEROGEN VANADATE IS IN A TRIGONAL BIPYRAMIDAL GEOMETRY AND THE VANADIUM ATOM IS COVALENTLY BONDED ...HETEROGEN VANADATE IS IN A TRIGONAL BIPYRAMIDAL GEOMETRY AND THE VANADIUM ATOM IS COVALENTLY BONDED TO SG ATOM OF CYS 403 WITH A BONDING DISTANCE OF 2.52 A.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tyrosine-protein phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6692
Polymers33,5541
Non-polymers1151
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.390, 49.660, 100.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Tyrosine-protein phosphatase / Virulence protein


Mass: 33553.883 Da / Num. of mol.: 1 / Fragment: Tyrosine-protein phosphatase / Mutation: C235R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia enterocolitica (bacteria) / Strain: W22703 / Gene: yopH, yop51 / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P15273, protein-tyrosine-phosphatase
#2: Chemical ChemComp-VO4 / VANADATE ION / Vanadate


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.26 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 400 mM NaCl, 14% PEG 4K, 5% 2-proponol .15% BME, 100mM Tris HCl pH 8.5, 1mM vanadate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Jan 1, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→10 Å / Num. all: 13593 / Num. obs: 13593 / % possible obs: 82 % / Observed criterion σ(I): 0 / Redundancy: 4.02 % / Rmerge(I) obs: 0.079
Reflection shellResolution: 2.1→2.3 Å / Redundancy: 2.14 % / Rmerge(I) obs: 0.25 / Num. unique all: 1336 / % possible all: 74.3

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
MADNESSdata collection
XSCALEdata scaling
X-PLOR3.1refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entries 1YTW and 1YTS

1ytw

1yts


Resolution: 2.2→7 Å / Isotropic thermal model: Isotropic / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: Residues Met163-Val186 were not included in the refinement due to missing electron densities.
RfactorNum. reflection
Rwork0.17 -
obs0.17 11701
Displacement parametersBiso mean: 17.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å / Luzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 2.2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 0 5 183 2354
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg2.2
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_improper_angle_d2.1
LS refinement shellResolution: 2.2→2.3 Å
RfactorNum. reflection% reflection
Rwork0.231 --
obs-1108 61.6 %

+
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