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- PDB-1vin: BOVINE CYCLIN A3 -

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Basic information

Entry
Database: PDB / ID: 1vin
TitleBOVINE CYCLIN A3
ComponentsCYCLIN A
KeywordsBINDING PROTEIN / CYCLIN / CELL CYCLE / KINASE-REGULATORY-SUBUNIT
Function / homology
Function and homology information


cell cycle G1/S phase transition / cyclin-dependent protein serine/threonine kinase regulator activity / cyclin A2-CDK2 complex / regulation of DNA replication / microtubule organizing center / cyclin-dependent protein kinase holoenzyme complex / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / cell division / nucleus / cytoplasm
Similarity search - Function
Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin-like / Cyclin, C-terminal domain / Cyclin_C ...Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin-like / Cyclin, C-terminal domain / Cyclin_C / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsNoble, M.E.M. / Endicott, J.A.E. / Brown, N.R.
Citation
#1: Journal: Structure / Year: 1995
Title: Two Structures of the Catalytic Domain of Phosphorylase Kinase: An Active Protein Kinase Complexed with Substrate Analogue and Product
Authors: Owen, D.J. / Noble, M.E.M. / Garman, E.F. / Papageorgiou, A.C. / Johnson, L.N.
#2: Journal: J.Mol.Biol. / Year: 1995
Title: Expression, Purification and Crystallisation of Phosphorylase Kinase Catalytic Domain
Authors: Owen, D.J. / Papageorgiou, A.C. / Garman, E.F. / Noble, M.E. / Johnson, L.N.
History
DepositionMar 15, 1996Processing site: BNL
Revision 1.0Aug 17, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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: CYCLIN A


Theoretical massNumber of molelcules
Total (without water)30,8321
Polymers30,8321
Non-polymers00
Water3,135174
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.700, 60.900, 83.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CYCLIN A


Mass: 30831.500 Da / Num. of mol.: 1 / Mutation: S171G, DEL(1-170)
Source method: isolated from a genetically manipulated source
Details: HIS 6 TAGGED AT C-TERMINUS / Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: BOVINE CYCLIN A3 / Plasmid: PET21D / Gene (production host): BOVINE CYCLIN A3 / Production host: Escherichia coli (E. coli) / References: UniProt: P30274
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 30 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-10 mg/mlcyclin A-31drop
20.1 M1dropMgCl2
30.01 %monothioglycerol1drop
40.01 %1dropNaN3
550 mMTris-HCl1drop
725-26 %methoxyPEG50001reservoir
80.2 M1reservoirLiSO4
90.1 MTris-HCl1reservoir
6reservoir1drop

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionNum. obs: 17065 / % possible obs: 91.4 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.068
Reflection
*PLUS
Highest resolution: 2 Å

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 2→6 Å / Rfactor Rfree: 0.299 / Rfactor Rwork: 0.216 / Rfactor obs: 0.216 / σ(F): 2
Displacement parametersBiso mean: 23.8 Å2
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2030 0 0 174 2204
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.84
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it5.58
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.41

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