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- PDB-1puc: P13SUC1 IN A STRAND-EXCHANGED DIMER -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1puc
TitleP13SUC1 IN A STRAND-EXCHANGED DIMER
ComponentsP13SUC1
KeywordsBINDING PROTEIN / CELL CYCLE / DOMAIN SWAPPING / STRAND-EXCHANGED DIMER
Function / homology
Function and homology information


signaling / cyclin-dependent protein serine/threonine kinase activator activity / SCF ubiquitin ligase complex / cyclin-dependent protein kinase holoenzyme complex / regulation of mitotic cell cycle / ubiquitin binding / histone binding / cell cycle / cell division / protein-containing complex binding ...signaling / cyclin-dependent protein serine/threonine kinase activator activity / SCF ubiquitin ligase complex / cyclin-dependent protein kinase holoenzyme complex / regulation of mitotic cell cycle / ubiquitin binding / histone binding / cell cycle / cell division / protein-containing complex binding / protein kinase binding / zinc ion binding / nucleus / cytosol
Similarity search - Function
Cyclin-Dependent Kinase Subunit Type 2 / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit / Cyclin-dependent kinase, regulatory subunit superfamily / Cyclin-dependent kinase regulatory subunit / Cyclin-dependent kinases regulatory subunits signature 1. / Cyclin-dependent kinases regulatory subunits signature 2. / Cyclin-dependent kinase regulatory subunit / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cyclin-dependent kinases regulatory subunit
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / Resolution: 1.95 Å
AuthorsKhazanovich, N. / Bateman, K.S. / Chernaia, M. / Michalak, M. / James, M.N.G.
CitationJournal: Structure / Year: 1996
Title: Crystal structure of the yeast cell-cycle control protein, p13suc1, in a strand-exchanged dimer.
Authors: Khazanovich, N. / Bateman, K. / Chernaia, M. / Michalak, M. / James, M.
History
DepositionDec 8, 1995Processing site: BNL
Revision 1.0Apr 3, 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 ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET EACH MOLECULE OF P13SUC1 IN THIS CRYSTAL PARTICIPATES IN A STRAND-EXCHANGED DIMER WITH A ...SHEET EACH MOLECULE OF P13SUC1 IN THIS CRYSTAL PARTICIPATES IN A STRAND-EXCHANGED DIMER WITH A SYMMETRY-RELATED MOLECULE. A SINGLE BETA-STRAND, ILE 94 - ASP 102, IS EXCHANGED BETWEEN THE CENTRAL BETA-SHEETS OF EACH MOLECULE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P13SUC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1872
Polymers12,5721
Non-polymers6151
Water1,29772
1
A: P13SUC1
hetero molecules

A: P13SUC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3744
Polymers25,1452
Non-polymers1,2302
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area4460 Å2
ΔGint-30.6 kcal/mol
Surface area14010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.270, 55.280, 111.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein P13SUC1 / P13


Mass: 12572.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Cell line: BL21 / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P08463
#2: Chemical ChemComp-CPS / 3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE / CHAPS / CHAPS detergent


Mass: 614.877 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H58N2O7S / Comment: detergent*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal grow
*PLUS
pH: 7.8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlrecombinant p13suc11drop
238 mM1dropLiCl
338 mMTris-HCl1drop
49 %(w/v)PEG MME 20001drop
50.4 %(w/v)CHAPS1drop
625 %(w/v)PEG MME 20001reservoir
70.1 M1reservoirLiCl
80.1 MTris-HCl1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Sep 28, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→55.9 Å / Num. obs: 9859 / % possible obs: 97.5 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.0488
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 53600 / Rmerge(I) obs: 0.0488
Reflection shell
*PLUS
Highest resolution: 1.95 Å / Lowest resolution: 1.98 Å / % possible obs: 81.4 %

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Processing

Software
NameVersionClassification
SDMSdata collection
X-PLOR3.1model building
TNTrefinement
X-PLOR3.1refinement
SDMSdata reduction
X-PLOR3.1phasing
RefinementResolution: 1.95→6 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.241 -10 %
obs0.187 8500 97.4 %
Displacement parametersBiso mean: 24 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.95→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms851 0 26 72 949
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.006
X-RAY DIFFRACTIONt_angle_deg1.422
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_deg24.472
X-RAY DIFFRACTIONt_improper_angle_d
X-RAY DIFFRACTIONt_improper_angle_deg1.192
X-RAY DIFFRACTIONt_plane_restr0.017

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