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- PDB-1sce: CRYSTAL STRUCTURE OF THE CELL CYCLE REGULATORY PROTEIN SUC1 REVEA... -

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Basic information

Entry
Database: PDB / ID: 1sce
TitleCRYSTAL STRUCTURE OF THE CELL CYCLE REGULATORY PROTEIN SUC1 REVEALS A NOVEL BETA-HINGE CONFORMATIONAL SWITCH
ComponentsSUC1
KeywordsCELL CYCLE REGULATORY PROTEIN
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: 2.2 Å
AuthorsBourne, Y. / Tainer, J.A.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Crystal structure of the cell cycle-regulatory protein suc1 reveals a beta-hinge conformational switch.
Authors: Bourne, Y. / Arvai, A.S. / Bernstein, S.L. / Watson, M.H. / Reed, S.I. / Endicott, J.E. / Noble, M.E. / Johnson, L.N. / Tainer, J.A.
#1: Journal: Embo J. / Year: 1995
Title: The Crystal Structure of P13Suc1, a P34Cdc2-Interacting Cell Cycle Control Protein
Authors: Endicott, J.E. / Noble, M.E. / Garman, E.F. / Brown, N. / Rasmussen, B. / Nurse, P. / Johnson, L.N.
History
DepositionMay 11, 1995Processing site: BNL
Revision 1.0Jan 29, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUC1
B: SUC1
C: SUC1
D: SUC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3797
Polymers53,2734
Non-polymers1063
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10640 Å2
ΔGint-83 kcal/mol
Surface area24630 Å2
MethodPISA
2
C: SUC1
hetero molecules

A: SUC1
B: SUC1
D: SUC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3797
Polymers53,2734
Non-polymers1063
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-59 kcal/mol
Surface area28190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.700, 85.600, 97.700
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
SUC1


Mass: 13318.138 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P08463
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal
*PLUS
Density % sol: 50 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %PEG40001reservoir
25 %sat1reservoirLiCl
3100 mMimidazole/malate1reservoir

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Data collection

ReflectionResolution: 2.2→30 Å / Num. obs: 19489 / % possible obs: 83 % / Observed criterion σ(I): 0
Reflection
*PLUS
Rmerge(I) obs: 0.06

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→6 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.284 --
Rwork0.193 --
obs0.193 18451 83 %
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3414 0 3 238 3655
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.5
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_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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