[English] 日本語
Yorodumi
- PDB-7l0m: Vanadate-bound YopH G352T -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7l0m
TitleVanadate-bound YopH G352T
ComponentsProtein-tyrosine-phosphatase
KeywordsHYDROLASE / Protein Tyrosine Phosphatase
Function / homology
Function and homology information


symbiont-mediated suppression of host reactive oxygen species generation / symbiont-mediated disruption of host focal adhesion / 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, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic ...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, 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
Similarity search - Domain/homology
VANADATE ION / protein-tyrosine-phosphatase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShen, R.D. / Hengge, A.C. / Johnson, S.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorR01GM112781 United States
CitationJournal: Jacs Au / Year: 2021
Title: Single Residue on the WPD-Loop Affects the pH Dependency of Catalysis in Protein Tyrosine Phosphatases.
Authors: Shen, R. / Crean, R.M. / Johnson, S.J. / Kamerlin, S.C.L. / Hengge, A.C.
History
DepositionDec 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein-tyrosine-phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7132
Polymers33,5981
Non-polymers1151
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.231, 56.091, 98.302
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Protein-tyrosine-phosphatase


Mass: 33597.938 Da / Num. of mol.: 1 / Mutation: G352T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria)
Gene: yopH, Y0013, YPCD1.67c, G4D65_20050, G4D67_19670, GD372_22270
Production host: Escherichia coli (E. coli) / References: UniProt: O68720, protein-tyrosine-phosphatase
#2: Chemical ChemComp-VO4 / VANADATE ION


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


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, and 15-34 % PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 18343 / % possible obs: 96.3 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.064 / Rrim(I) all: 0.189 / Χ2: 1.037 / Net I/σ(I): 6.3 / Num. measured all: 140771
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0750.64815360.7960.2780.711.03382.5
2.07-2.156.20.50816690.9280.1930.5471.08889.3
2.15-2.256.70.46817660.9240.1760.5031.06894.6
2.25-2.377.20.43518130.9470.1630.4661.01197.5
2.37-2.527.50.36118710.970.1370.3881.0499.3
2.52-2.718.80.30318840.9760.1040.3211.09299.9
2.71-2.998.80.22418980.9870.0780.2381.03199.9
2.99-3.428.40.1819180.9870.0640.1921.04199.9
3.42-4.3190.13719200.9920.0460.1451.02699.8
4.31-508.30.11120680.9930.040.1180.96799.9

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YAA

4yaa


Resolution: 2→49.15 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2263 914 5 %
Rwork0.178 17355 -
obs0.1805 18269 95.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.19 Å2 / Biso mean: 32.4515 Å2 / Biso min: 16.97 Å2
Refinement stepCycle: final / Resolution: 2→49.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2112 0 5 142 2259
Biso mean--28.15 35.72 -
Num. residues----282
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.10.30581080.25652046215481
2.1-2.240.22531250.21212354247992
2.24-2.410.29471310.20452490262197
2.41-2.650.25131330.186325302663100
2.65-3.030.22381350.186925782713100
3.03-3.820.20821380.165126212759100
3.82-49.150.20231440.154327362880100
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)
12.0410.19560.2842.68951.04565.3508-0.05420.3135-0.1591-0.2814-0.0669-0.20870.24970.36440.08760.27210.04580.06480.22550.02770.3932-13.499218.1524-41.1361
21.89790.2115-0.1873.3941-0.89941.42520.0548-0.12730.37170.2463-0.04020.0987-0.17050.0432-0.00870.1520.00110.0120.1695-0.05180.2697-12.338315.85-14.4954
31.34140.425-0.05550.29320.02461.18310.007-0.0448-0.0180.0109-0.0381-0.05440.09360.02520.02240.24340.0134-0.00330.1955-0.01910.3865-14.1819-0.8509-14.2298
43.35780.4277-0.6881.38221.63642.38580.2486-0.3150.77080.66290.0931.6533-0.8783-1.3867-0.36110.3720.14680.11570.57090.04030.7192-30.345210.1543-10.7979
50.79530.01310.68271.1179-0.07661.8977-0.03370.05350.1403-0.1714-0.05410.1046-0.0122-0.06590.07860.2240.01160.00780.1998-0.0270.3539-17.874411.0239-30.8333
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 187 through 208 )A187 - 208
2X-RAY DIFFRACTION2chain 'A' and (resid 209 through 287 )A209 - 287
3X-RAY DIFFRACTION3chain 'A' and (resid 288 through 385 )A288 - 385
4X-RAY DIFFRACTION4chain 'A' and (resid 386 through 398 )A386 - 398
5X-RAY DIFFRACTION5chain 'A' and (resid 399 through 468 )A399 - 468

+
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