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- PDB-1c25: HUMAN CDC25A CATALYTIC DOMAIN -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1c25
TitleHUMAN CDC25A CATALYTIC DOMAIN
ComponentsCDC25A
KeywordsHYDROLASE / CELL CYCLE PHOSPHATASE / DUAL SPECIFICITY PROTEIN PHOSPHATASE / CDK2
Function / homology
Function and homology information


positive regulation of G2/MI transition of meiotic cell cycle / Transcription of E2F targets under negative control by DREAM complex / Polo-like kinase mediated events / regulation of cyclin-dependent protein serine/threonine kinase activity / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / phosphoprotein phosphatase activity / Activation of ATR in response to replication stress / Cyclin E associated events during G1/S transition / 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 / Transcription of E2F targets under negative control by DREAM complex / Polo-like kinase mediated events / regulation of cyclin-dependent protein serine/threonine kinase activity / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / phosphoprotein phosphatase activity / Activation of ATR in response to replication stress / Cyclin E associated events during G1/S transition / 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 / positive regulation of DNA replication / protein tyrosine phosphatase activity / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / response to radiation / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / cellular response to UV / protein-folding chaperone binding / cell population proliferation / Ub-specific processing proteases / cell division / 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
M-phase inducer phosphatase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.3 Å
AuthorsFauman, E.B. / Cogswell, J.P. / Lovejoy, B. / Rocque, W.J. / Holmes, W. / Montana, V.G. / Piwnica-Worms, H. / Rink, M.J. / Saper, M.A.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1998
Title: Crystal structure of the catalytic domain of the human cell cycle control phosphatase, Cdc25A.
Authors: Fauman, E.B. / Cogswell, J.P. / Lovejoy, B. / Rocque, W.J. / Holmes, W. / Montana, V.G. / Piwnica-Worms, H. / Rink, M.J. / Saper, M.A.
History
DepositionApr 17, 1998Processing site: BNL
Revision 1.0Aug 19, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CDC25A


Theoretical massNumber of molelcules
Total (without water)19,0111
Polymers19,0111
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.507, 43.507, 117.096
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein CDC25A / M-PHASE INDUCER PHOSPHATASE 1


Mass: 19010.982 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN / Mutation: INS(M335)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Cellular location: CYTOPLASM / Gene: CDC25A / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P30304, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 40 %
Crystal growpH: 5.8
Details: 4 MICROLITERS PROTEIN (10 MG/ML IN 200 MM NACL, 1 MM DTT, 20 MM HEPES, PH 7.4) MIXED WITH 4 MICROLITERS WELL BUFFER (18-20% PEG 3350, 0.025% BETA-OCTYLGLUCOSIDE, 0.11 M SODIUM CITRATE, PH 5.8)
PH range: 5.8-7.4
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
2200 mM1dropNaCl
31 mMdithiothreitol1drop
420 mMHEPES1drop
518-20 %PEG33501reservoir
60.025 %beta-octylglucoside1reservoir
70.11 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.1 Å / Num. obs: 12551 / % possible obs: 98.3 % / Redundancy: 3 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 18
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 3 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 3 / Rsym value: 0.372 / % possible all: 100
Reflection
*PLUS
Num. measured all: 39374
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MIR / Resolution: 2.3→99 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.296 467 5 %RANDOM
Rwork0.227 ---
obs0.227 9429 97.8 %-
Displacement parametersBiso mean: 36 Å2
Refinement stepCycle: LAST / Resolution: 2.3→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1329 0 0 82 1411
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.59
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.54
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it11.5
X-RAY DIFFRACTIONx_mcangle_it1.92
X-RAY DIFFRACTIONx_scbond_it11.5
X-RAY DIFFRACTIONx_scangle_it1.92
LS refinement shellResolution: 2.3→2.33 Å / Rfactor Rfree error: 0.107 / Total num. of bins used: 30
RfactorNum. reflection% reflection
Rfree0.429 16 5 %
Rwork0.339 290 -
obs--99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATPARAM11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.54

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