[English] 日本語
Yorodumi
- PDB-2uzq: Protein Phosphatase, New Crystal Form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2uzq
TitleProtein Phosphatase, New Crystal Form
ComponentsM-PHASE INDUCER PHOSPHATASE 2
KeywordsHYDROLASE / CELL DIVISION / PHOSPHORYLATION / DUAL SPECIFICITY / MITOSIS / CELL CYCLE / PHOSPHATASE / PROTEIN PHOSPHATASE
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 / positive regulation of G2/M transition of mitotic cell cycle / 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/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 / positive regulation of G2/M transition of mitotic cell cycle / 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 / protein-tyrosine-phosphatase / positive regulation of mitotic cell cycle / protein tyrosine phosphatase activity / G2/M transition of mitotic cell cycle / spindle pole / mitotic cell cycle / protein phosphorylation / cell division / positive regulation of cell population proliferation / centrosome / protein kinase binding / nucleoplasm / nucleus / cytoplasm / cytosol
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
PHOSPHATE ION / M-phase inducer phosphatase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsHillig, R.C. / Eberspaecher, U.
Citation
Journal: To be Published
Title: New Crystal Form of Protein Phosphatase Cdc25B Triggered by Guanidinium Chloride as an Additive
Authors: Hillig, R.C. / Eberspaecher, U.
#1: Journal: Biochemistry / Year: 2005
Title: Experimental Validation of the Docking Orientation of Cdc25 with its Cdk2-Cyca Protein Substrate.
Authors: Sohn, J. / Parks, J.M. / Buhrman, G. / Brown, P. / Kristjansdottir, K. / Safi, A. / Edelsbrunner, H. / Yang, W. / Rudolph, J.
#2: Journal: 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, M.R.J. / Chidester, C.G. / Watenpaugh, K.D.
History
DepositionMay 1, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: M-PHASE INDUCER PHOSPHATASE 2
B: M-PHASE INDUCER PHOSPHATASE 2
C: M-PHASE INDUCER PHOSPHATASE 2
D: M-PHASE INDUCER PHOSPHATASE 2
E: M-PHASE INDUCER PHOSPHATASE 2
F: M-PHASE INDUCER PHOSPHATASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,27512
Polymers140,7056
Non-polymers5706
Water3,531196
1
A: M-PHASE INDUCER PHOSPHATASE 2
B: M-PHASE INDUCER PHOSPHATASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0924
Polymers46,9022
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-5.6 kcal/mol
Surface area20460 Å2
MethodPQS
2
C: M-PHASE INDUCER PHOSPHATASE 2
D: M-PHASE INDUCER PHOSPHATASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0924
Polymers46,9022
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-7.4 kcal/mol
Surface area20280 Å2
MethodPQS
3
E: M-PHASE INDUCER PHOSPHATASE 2
F: M-PHASE INDUCER PHOSPHATASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0924
Polymers46,9022
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-7.2 kcal/mol
Surface area20420 Å2
MethodPQS
Unit cell
Length a, b, c (Å)123.925, 123.925, 174.035
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99922, -0.00332, -0.03927), (0.00389, -0.99989, -0.01446), (-0.03921, -0.0146, 0.99912)63.3389, 176.33797, 2.37184
2given(0.5764, -0.8167, 0.02771), (0.81614, 0.57705, 0.03061), (-0.04098, 0.00497, 0.99915)54.98053, -41.32238, 22.6779
3given(-0.58725, 0.8094, 0.00139), (-0.80845, -0.58647, -0.04959), (-0.03932, -0.03025, 0.99877)-51.85634, 112.94102, 25.71187
4given(0.98738, 0.07916, 0.13718), (-0.0887, 0.99395, 0.06484), (-0.13122, -0.07619, 0.98842)-69.33879, -31.47198, 6.67416
5given(-0.99493, -0.04044, 0.09203), (0.0453, -0.99765, 0.05132), (0.08974, 0.05523, 0.99443)3.75284, 140.10407, -11.50927

-
Components

#1: Protein
M-PHASE INDUCER PHOSPHATASE 2 / DUAL SPECIFICITY PHOSPHATASE CDC25B / CDC25B


Mass: 23450.812 Da / Num. of mol.: 6 / Fragment: CATALYTIC DOMAIN, RESIDUES 377-566
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P30305, protein-tyrosine-phosphatase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE CONTAINS N-TERMINAL RESIDUES WHICH REPRESENT A CLONING ARTIFACT (THROMBIN CLEAVAGE SITE ...SEQUENCE CONTAINS N-TERMINAL RESIDUES WHICH REPRESENT A CLONING ARTIFACT (THROMBIN CLEAVAGE SITE AND POLY GLY LINKER, GSPGIS GGGGG). OUT OF THE FOUR ISOFORM SEQUENCES GENERATED BY ALTERNATE SPLICING, THE ENTRY BELONGS TO ISOFORM 1

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 53.4 %
Crystal growpH: 7 / Details: PEG 8000, HEPES PH 7.0, GUANIDINIUM CHLORIDE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.95368
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 30, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95368 Å / Relative weight: 1
ReflectionResolution: 2.38→36.8 Å / Num. obs: 58835 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.05
Reflection shellResolution: 2.38→2.47 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.5 / % possible all: 89.3

-
Processing

Software
NameVersionClassification
CNX2002refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QB0

1qb0


Resolution: 2.38→36.77 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.249 3108 5.3 %RANDOM
Rwork0.226 ---
obs-58824 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.1889 Å2 / ksol: 0.355341 e/Å3
Displacement parametersBiso mean: 54 Å2
Baniso -1Baniso -2Baniso -3
1-2.95 Å29.68 Å20 Å2
2--2.95 Å20 Å2
3----5.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.38→36.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8472 0 30 196 8698
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.42
X-RAY DIFFRACTIONc_mcangle_it2.413
X-RAY DIFFRACTIONc_scbond_it1.94.5
X-RAY DIFFRACTIONc_scangle_it2.926
Refine LS restraints NCSNCS model details: NCS RESTRAINTS
LS refinement shellResolution: 2.38→2.47 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10 /
Rfactor% reflection
Rfree0.34 4.7 %
Rwork0.308 -
obs-88.6 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: ION.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