[English] 日本語
Yorodumi
- PDB-1wrm: Crystal structure of JSP-1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1wrm
TitleCrystal structure of JSP-1
Componentsdual specificity phosphatase 22
KeywordsHYDROLASE / phosphatase / DSP / JNK
Function / homology
Function and homology information


negative regulation of T cell mediated immunity / leading edge of lamellipodium / protein tyrosine/serine/threonine phosphatase activity / negative regulation of focal adhesion assembly / negative regulation of T cell activation / protein tyrosine kinase inhibitor activity / negative regulation of T cell receptor signaling pathway / protein-serine/threonine phosphatase / filamentous actin / protein serine/threonine phosphatase activity ...negative regulation of T cell mediated immunity / leading edge of lamellipodium / protein tyrosine/serine/threonine phosphatase activity / negative regulation of focal adhesion assembly / negative regulation of T cell activation / protein tyrosine kinase inhibitor activity / negative regulation of T cell receptor signaling pathway / protein-serine/threonine phosphatase / filamentous actin / protein serine/threonine phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / immune system process / protein-tyrosine-phosphatase / transforming growth factor beta receptor signaling pathway / protein tyrosine phosphatase activity / protein tyrosine kinase binding / cellular response to epidermal growth factor stimulus / negative regulation of cell migration / positive regulation of JNK cascade / regulation of cell population proliferation / intracellular signal transduction / negative regulation of transcription by RNA polymerase II / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like ...Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / 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 22
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsYokota, T. / Kashima, A. / Kato, R. / Sugio, S.
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of human dual specificity phosphatase, JNK stimulatory phosphatase-1, at 1.5 A resolution
Authors: Yokota, T. / Nara, Y. / Kashima, A. / Matsubara, K. / Misawa, S. / Kato, R. / Sugio, S.
History
DepositionOct 22, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: dual specificity phosphatase 22
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8762
Polymers18,6811
Non-polymers1951
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.027, 49.320, 47.330
Angle α, β, γ (deg.)90.00, 119.51, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein dual specificity phosphatase 22 / LMW-DSP2 / mitogen-activated protein kinase phosphatase x / JNK-stimulating phosphatase 1


Mass: 18681.258 Da / Num. of mol.: 1 / Fragment: residues 1-163
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET32-a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE4)-RP / References: UniProt: Q9NRW4, protein-tyrosine-phosphatase
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.4 Å3/Da / Density % sol: 49.4 %
Crystal growTemperature: 278 K / Method: vapor diffusion / pH: 6.8
Details: PEG4000, magnesium chloride, MES-NaOH, pH 6.8, VAPOR DIFFUSION, temperature 278K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL24XU / Wavelength: 0.83565 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 21, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.83565 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 24804 / Num. obs: 24754 / % possible obs: 91.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 37.8
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 4.1 / % possible all: 83.9

-
Processing

Software
NameVersionClassification
CNX2002refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→40.89 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1192695.44 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1201 4.9 %RANDOM
Rwork0.251 ---
all-24754 --
obs-23553 91.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.4755 Å2 / ksol: 0.361237 e/Å3
Displacement parametersBiso mean: 30.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.44 Å20 Å2-13.35 Å2
2---6.81 Å20 Å2
3---3.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.64 Å0.69 Å
Refinement stepCycle: LAST / Resolution: 1.5→40.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1244 0 12 80 1336
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_improper_angle_d0.71
LS refinement shellHighest resolution: 1.5 Å / Total num. of bins used: 6 /
Num. reflection% reflection
Rwork3022 -
Rfree-5.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5MES.PARAMMES.TOP

+
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