[English] 日本語
Yorodumi
- PDB-6i28: Crystal Structure of Cydia Pomonella PTP-2 phosphatase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6i28
TitleCrystal Structure of Cydia Pomonella PTP-2 phosphatase
ComponentsORF98 PTP-2
KeywordsVIRAL PROTEIN / Cydia Pomonella / PTP-2 phosphatase
Function / homology
Function and homology information


protein tyrosine/serine/threonine phosphatase activity / protein tyrosine phosphatase activity
Similarity search - Function
Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / 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
Similarity search - Domain/homology
Biological speciesCydia pomonella granulosis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 1.65 Å
AuthorsHuang, G. / Keown, J.P. / Oliver, M.R. / Metcalf, P.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of New ZealandUOA221 New Zealand
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Crystal structure of protein tyrosine phosphatase-2 from Cydia pomonella granulovirus.
Authors: Huang, G. / Oliver, M.R. / Keown, J.R. / Goldstone, D.C. / Metcalf, P.
History
DepositionOct 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / pdbx_database_proc
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ORF98 PTP-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6103
Polymers19,4781
Non-polymers1322
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-12 kcal/mol
Surface area8240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.690, 66.720, 97.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-317-

HOH

-
Components

#1: Protein ORF98 PTP-2


Mass: 19478.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cydia pomonella granulosis virus / Strain: isolate Mexico/1963 / Gene: orf98 ptp-2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q91EV7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.85 Å3/Da / Density % sol: 56.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: HEPES-NaOH pH 7.5, 200mM CaCl2, 14%-20% PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.65→46.44 Å / Num. obs: 25886 / % possible obs: 100 % / Redundancy: 14.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.047 / Rrim(I) all: 0.178 / Net I/σ(I): 11.2 / Num. measured all: 365717 / Scaling rejects: 140
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.65-1.6814.23.93712500.4041.0824.085100
9.04-46.4410.50.0331910.9990.010.03498.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.38 Å33.7 Å
Translation5.38 Å33.7 Å

-
Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHASER2.7.17phasing
PHENIX1.14refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.65→33.702 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.62
RfactorNum. reflection% reflection
Rfree0.2239 1307 5.05 %
Rwork0.1852 --
obs0.1872 25882 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 149.04 Å2 / Biso mean: 37.4873 Å2 / Biso min: 13.18 Å2
Refinement stepCycle: final / Resolution: 1.65→33.702 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1302 0 14 110 1426
Biso mean--68.39 43.45 -
Num. residues----161
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.65-1.71610.40911550.36526682823
1.7161-1.79420.38851390.33727052844
1.7942-1.88880.31321380.297526892827
1.8888-2.00710.35291150.242227272842
2.0071-2.16210.2521120.203127542866
2.1621-2.37960.24121470.165527112858
2.3796-2.72380.21391410.163327382879
2.7238-3.43120.19171760.167927372913
3.4312-33.70870.18541840.146728463030

+
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://pdbjlvh1.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