[English] 日本語
Yorodumi
- PDB-2q05: Crystal structure of tyr/ser protein phosphatase from Vaccinia vi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2q05
TitleCrystal structure of tyr/ser protein phosphatase from Vaccinia virus WR
ComponentsDual specificity protein phosphatase
KeywordsHYDROLASE / phosphatase / Vaccinia virus / structural genomics / APC7320 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / negative regulation of MAPK cascade / protein serine/threonine phosphatase activity / phosphatase activity / dephosphorylation / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / protein-tyrosine-phosphatase ...MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / MAP kinase tyrosine/serine/threonine phosphatase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / negative regulation of MAPK cascade / protein serine/threonine phosphatase activity / phosphatase activity / dephosphorylation / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / protein-tyrosine-phosphatase / virion component / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / cytoplasm
Similarity search - Function
Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. ...Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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
Dual specificity protein phosphatase OPG106
Similarity search - Component
Biological speciesVaccinia virus WR
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.57 Å
AuthorsOsipiuk, J. / Skarina, T. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of tyr/ser protein phosphatase from Vaccinia virus WR.
Authors: Osipiuk, J. / Skarina, T. / Kagan, O. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionMay 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS EXPERIMENTALLY UNKNOWN. THE DODECAMERIC ASSEMBLY OF THE BIOLOGICAL UNIT, SHOWN IN REMARK 350, IS PREDICTED BY THE ANALYSIS OF PROTEIN INTERFACES (PISA) BASED ON THIS CRYSTAL STRUCTURE.
Remark 999 SEQUENCE AUTHORS STATE THAT THE ELECTRON DENSITY CLEARLY SHOWS THE PRESENCE OF ARGININE AT ... SEQUENCE AUTHORS STATE THAT THE ELECTRON DENSITY CLEARLY SHOWS THE PRESENCE OF ARGININE AT SEQUENCE POSITION 20 IN ALL FOUR CHAINS A-D IN THE ASYMMETRIC UNIT. THE PRESENCE OF ARGININES IS SUPPORTED BY OMIT MAPS AND BY THE R-FACTOR INCREASE WHEN LYSINES ARE BEING REFINED AT THAT POSITION.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dual specificity protein phosphatase
B: Dual specificity protein phosphatase
C: Dual specificity protein phosphatase
D: Dual specificity protein phosphatase


Theoretical massNumber of molelcules
Total (without water)91,7434
Polymers91,7434
Non-polymers00
Water1,13563
1
A: Dual specificity protein phosphatase
B: Dual specificity protein phosphatase
C: Dual specificity protein phosphatase
D: Dual specificity protein phosphatase

A: Dual specificity protein phosphatase
B: Dual specificity protein phosphatase
C: Dual specificity protein phosphatase
D: Dual specificity protein phosphatase

A: Dual specificity protein phosphatase
B: Dual specificity protein phosphatase
C: Dual specificity protein phosphatase
D: Dual specificity protein phosphatase


Theoretical massNumber of molelcules
Total (without water)275,22912
Polymers275,22912
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_645-z+1,x-1/2,-y+1/21
crystal symmetry operation11_556y+1/2,-z+1/2,-x+11
Buried area31360 Å2
ΔGint-215 kcal/mol
Surface area84500 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)169.246, 169.246, 169.246
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

-
Components

#1: Protein
Dual specificity protein phosphatase / Late protein H1


Mass: 22935.723 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus WR / Genus: Orthopoxvirus / Species: Vaccinia virusVaccinia / Strain: WR (Western Reserve), VACV / Gene: H1L, VACWR099 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P07239, protein-tyrosine-phosphatase, protein-serine/threonine phosphatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 4.4 Å3/Da / Density % sol: 72.06 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 2M Sodium acetate pH 7.0, B-propane buffer pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 25, 2007
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.57→40 Å / Num. all: 51445 / Num. obs: 51445 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22.5 % / Biso Wilson estimate: 65.5 Å2 / Rmerge(I) obs: 0.133 / Net I/σ(I): 35.5
Reflection shellResolution: 2.57→2.66 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.899 / Mean I/σ(I) obs: 2.21 / Num. unique all: 4979 / % possible all: 97.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.57→40 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.93 / SU B: 13.217 / SU ML: 0.137 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.24 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Only fragments of N-terminal parts (His-tags) of chains A and D were identified in the electron density and modeled with the side chain atoms missing.
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 2610 5.1 %RANDOM
Rwork0.1913 ---
all0.1927 48741 --
obs0.1927 48741 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.961 Å2
Refinement stepCycle: LAST / Resolution: 2.57→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5738 0 0 63 5801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225887
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.9667951
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8115715
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.16823.779262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.445151081
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8851532
X-RAY DIFFRACTIONr_chiral_restr0.110.2888
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024361
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.22561
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.24003
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2216
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2630.274
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0910.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9821.53657
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48425806
X-RAY DIFFRACTIONr_scbond_it2.30932514
X-RAY DIFFRACTIONr_scangle_it3.324.52141
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.57→2.637 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 170 -
Rwork0.328 3490 -
obs-3660 96.93 %

+
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