[English] 日本語
Yorodumi
- PDB-1cwr: HUMAN CDC25B CATALYTIC DOMAIN WITHOUT ION IN CATALYTIC SITE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cwr
TitleHUMAN CDC25B CATALYTIC DOMAIN WITHOUT ION IN CATALYTIC SITE
ComponentsPROTEIN (M-PHASE INDUCER PHOSPHATASE 2 (CDC25B))
KeywordsHYDROLASE / CELL CYCLE PHOSPHATASE / DUAL SPECIFICITY PROTEIN PHOSPHATASE / CDC25 / CDC25B
Function / homology
Function and homology information


positive regulation of G2/MI transition of meiotic cell cycle / oocyte maturation / female meiosis I / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / positive regulation of cytokinesis / phosphoprotein phosphatase activity / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / positive regulation of G2/M transition of mitotic cell cycle ...positive regulation of G2/MI transition of meiotic cell cycle / oocyte maturation / female meiosis I / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / positive regulation of cytokinesis / phosphoprotein phosphatase activity / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / positive regulation of G2/M transition of mitotic cell cycle / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / positive regulation of mitotic cell cycle / spindle pole / G2/M transition of mitotic cell cycle / mitotic cell cycle / protein phosphorylation / cell division / positive regulation of cell population proliferation / centrosome / protein kinase binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
M-phase inducer phosphatase / M-phase inducer phosphatase / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / M-phase inducer phosphatase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.1 Å
AuthorsWatenpaugh, K.D. / Reynolds, R.A. / Chidester, C.G.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of the catalytic subunit of Cdc25B required for G2/M phase transition of the cell cycle.
Authors: Reynolds, R.A. / Yem, A.W. / Wolfe, C.L. / Deibel Jr., M.R. / Chidester, C.G. / Watenpaugh, K.D.
History
DepositionAug 26, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 6, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTEIN (M-PHASE INDUCER PHOSPHATASE 2 (CDC25B))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0823
Polymers24,9071
Non-polymers1742
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.733, 71.110, 75.247
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein PROTEIN (M-PHASE INDUCER PHOSPHATASE 2 (CDC25B))


Mass: 24907.461 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Gene: CDC25B / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P30305, protein-tyrosine-phosphatase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.78 Å3/Da / Density % sol: 55.71 %
Crystal growpH: 9
Details: 4 MICROLITERS PROTEIN (10 MG/ ML IN 50 MM TRISHCL, 1% BME AT PH 9.0) MIXED WITH 4 MICROLITERS WELL BUFFER (1.8 (NH4)2SO4, 0.5 M NACL, 0.1 M TRISHCL, 0.25 BME) AT 4 DEG. C
Crystal grow
*PLUS
Temperature: 4.0 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
250 mMTris-HCl1drop
31 %(v/v)beta-mercaptoethanol1drop
41.8 Mammonium sulfate1reservoir
50.5 M1reservoirNaCl
60.1 MTris-HCl1reservoir
70.25 %BME1reservoir

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS HI-STAR / Detector: AREA DETECTOR / Date: Apr 6, 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 15943 / % possible obs: 80.44 % / Observed criterion σ(I): 0 / Redundancy: 1.75 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 20.1
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 1.6 / % possible all: 30
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 15237 / % possible obs: 90.1 % / Num. measured all: 26953 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / % possible obs: 70.7 % / Mean I/σ(I) obs: 2.3 / Rmerge(I) obs: 0.23

-
Processing

Software
NameVersionClassification
SADIEdata collection
SAINTdata reduction
XTAL3.0model building
SHELXL-97refinement
SADIEdata reduction
SAINTdata scaling
XTALV. 3.0phasing
RefinementMethod to determine structure: MIR / Resolution: 2.1→10 Å / σ(F): 4 / Stereochemistry target values: ENGH & HUBER
Details: RESIDUES CYS A 426, CYS A 474; AND ARG A 479 EACH HAVE TWO ALTERNATIVE CONFORMATIONS MODELED. CYS 426 AND CYS 473 FORM A DISULFIDE APROXIMATELY 50 PERCENT OF THE TIME.
RfactorNum. reflection% reflection
obs0.204 -90.1 %
all-14723 -
Refine analyzeNum. disordered residues: 3
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1484 0 9 103 1596
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.03
X-RAY DIFFRACTIONs_angle_d0.2
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 4 / Num. reflection Rfree: 594 / Rfactor all: 0.202 / Rfactor obs: 0.175 / Rfactor Rfree: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.4

+
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