[English] 日本語
Yorodumi
- PDB-7y4c: Crystal structure of DUSP10 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7y4c
TitleCrystal structure of DUSP10
ComponentsDual specificity protein phosphatase 10
KeywordsHYDROLASE / Dual specificity protein phosphatase 10 / MAP kinase phosphatase 5
Function / homology
Function and homology information


negative regulation of epithelium regeneration / MAP kinase phosphatase activity / MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / regulation of adaptive immune response / MAP kinase tyrosine/serine/threonine phosphatase activity / regulation of brown fat cell differentiation / negative regulation of p38MAPK cascade / negative regulation of epithelial cell migration / peptidyl-threonine dephosphorylation ...negative regulation of epithelium regeneration / MAP kinase phosphatase activity / MAP kinase tyrosine phosphatase activity / protein tyrosine/threonine phosphatase activity / regulation of adaptive immune response / MAP kinase tyrosine/serine/threonine phosphatase activity / regulation of brown fat cell differentiation / negative regulation of p38MAPK cascade / negative regulation of epithelial cell migration / peptidyl-threonine dephosphorylation / Signaling by MAPK mutants / negative regulation of oligodendrocyte differentiation / negative regulation of JUN kinase activity / RAF-independent MAPK1/3 activation / negative regulation of JNK cascade / JUN kinase binding / positive regulation of regulatory T cell differentiation / negative regulation of stress-activated MAPK cascade / myosin phosphatase activity / mitogen-activated protein kinase p38 binding / peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity / protein-serine/threonine phosphatase / oligodendrocyte differentiation / phosphatase activity / negative regulation of respiratory burst involved in inflammatory response / stress-activated MAPK cascade / dephosphorylation / negative regulation of cell migration / protein-tyrosine-phosphatase / negative regulation of ERK1 and ERK2 cascade / Negative regulation of MAPK pathway / negative regulation of epithelial cell proliferation / response to lipopolysaccharide / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Mitogen-activated protein (MAP) kinase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily ...Mitogen-activated protein (MAP) kinase phosphatase / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Rhodanese Homology Domain / Dual specificity protein phosphatase domain / Dual specificity protein phosphatase domain profile. / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 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
Dual specificity protein phosphatase 10
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsHu, I.C. / Lyu, P.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: To Be Published
Title: Crystal structure of DUSP10
Authors: Hu, I.C. / Lyu, P.C.
History
DepositionJun 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Dual specificity protein phosphatase 10
B: Dual specificity protein phosphatase 10
C: Dual specificity protein phosphatase 10
D: Dual specificity protein phosphatase 10


Theoretical massNumber of molelcules
Total (without water)68,4944
Polymers68,4944
Non-polymers00
Water7,422412
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.235, 56.128, 69.594
Angle α, β, γ (deg.)92.010, 92.280, 105.280
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein
Dual specificity protein phosphatase 10 / Mitogen-activated protein kinase phosphatase 5 / MAP kinase phosphatase 5 / MKP-5


Mass: 17123.568 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUSP10, MKP5
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9Y6W6, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25% (w/v) PEG 3000, 100 mM Tris base /Hydrochloric acid, 175 mM Calcium acetate
PH range: 6.8-7.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→30 Å / Num. obs: 49102 / % possible obs: 96.6 % / Redundancy: 2 % / Biso Wilson estimate: 24.51 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 10.591
Reflection shellResolution: 1.87→1.94 Å / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 3.852 / Num. unique obs: 48593

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZZW

1zzw


Resolution: 1.87→24.38 Å / SU ML: 0.1322 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 45.0724
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2675 1984 4.08 %
Rwork0.2184 46609 -
obs0.2204 48593 95.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.82 Å2
Refinement stepCycle: LAST / Resolution: 1.87→24.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4816 0 0 412 5228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01094920
X-RAY DIFFRACTIONf_angle_d1.10246652
X-RAY DIFFRACTIONf_chiral_restr0.058732
X-RAY DIFFRACTIONf_plane_restr0.01868
X-RAY DIFFRACTIONf_dihedral_angle_d7.1607648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.920.3581310.29543216X-RAY DIFFRACTION90.85
1.92-1.970.31911380.26973273X-RAY DIFFRACTION95.31
1.97-2.020.28721460.25383391X-RAY DIFFRACTION95.67
2.02-2.090.31041420.23963328X-RAY DIFFRACTION95.88
2.09-2.160.2951420.22913333X-RAY DIFFRACTION95.76
2.16-2.250.25011460.23023368X-RAY DIFFRACTION96.09
2.25-2.350.25291340.21983376X-RAY DIFFRACTION96.3
2.35-2.480.28371530.22153342X-RAY DIFFRACTION96.41
2.48-2.630.28611390.21873381X-RAY DIFFRACTION96.54
2.63-2.840.27271490.22573365X-RAY DIFFRACTION96.94
2.84-3.120.31651410.23543403X-RAY DIFFRACTION97.36
3.12-3.570.30981470.20773374X-RAY DIFFRACTION96.55
3.57-4.490.23441460.18333321X-RAY DIFFRACTION95.35
4.49-24.380.18631300.2083138X-RAY DIFFRACTION89.46
Refinement TLS params.Method: refined / Origin x: -6.33037917569 Å / Origin y: -10.49783716 Å / Origin z: -15.4964755509 Å
111213212223313233
T0.141062166662 Å20.0162032885768 Å2-0.000435183449755 Å2-0.157409449045 Å20.00465953717421 Å2--0.177513413763 Å2
L0.224370613979 °20.217922398226 °20.027671540135 °2-0.449047663849 °20.0236572680454 °2--0.0403821811282 °2
S0.0234350471968 Å °-0.0668114037669 Å °0.00643285860059 Å °-0.104254946751 Å °-0.0245265843021 Å °0.000889167745662 Å °0.00730684167632 Å °-0.00295775152347 Å °0.00042946721664 Å °
Refinement TLS groupSelection details: all

+
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