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- PDB-1uii: Crystal structure of Geminin coiled-coil domain -

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Basic information

Entry
Database: PDB / ID: 1uii
TitleCrystal structure of Geminin coiled-coil domain
ComponentsGeminin
KeywordsCELL CYCLE / GEMININ / HUMAN / DNA REPLICATION
Function / homology
Function and homology information


DNA replication preinitiation complex assembly / Switching of origins to a post-replicative state / negative regulation of DNA-templated DNA replication / positive regulation of chromatin binding / regulation of DNA-templated DNA replication initiation / negative regulation of DNA replication / regulation of DNA replication / negative regulation of cell cycle / Activation of the pre-replicative complex / regulation of mitotic cell cycle ...DNA replication preinitiation complex assembly / Switching of origins to a post-replicative state / negative regulation of DNA-templated DNA replication / positive regulation of chromatin binding / regulation of DNA-templated DNA replication initiation / negative regulation of DNA replication / regulation of DNA replication / negative regulation of cell cycle / Activation of the pre-replicative complex / regulation of mitotic cell cycle / transcription repressor complex / Assembly of the pre-replicative complex / animal organ morphogenesis / histone deacetylase binding / transcription corepressor activity / DNA-binding transcription factor binding / negative regulation of DNA-templated transcription / chromatin binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Geminin/Multicilin / Geminin / Geminin coiled-coil domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsYuan, P. / Swaminathan, K. / Robinson, H.
CitationJournal: Mol.Cell / Year: 2004
Title: A dimerized coiled-coil domain and an adjoining part of geminin interact with two sites on Cdt1 for replication inhibition
Authors: Saxena, S. / Yuan, P. / Dhar, S.K. / Senga, T. / Takeda, D. / Robinson, H. / Kornbluth, S. / Swaminathan, K. / Dutta, A.
History
DepositionJul 16, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Geminin
B: Geminin


Theoretical massNumber of molelcules
Total (without water)19,5302
Polymers19,5302
Non-polymers00
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-24 kcal/mol
Surface area9610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.160, 94.460, 102.560
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 Geminin /


Mass: 9764.943 Da / Num. of mol.: 2 / Fragment: coiled-coil domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GMNN / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)LYS-S / References: UniProt: O75496
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.6 Å3/Da / Density % sol: 65.3 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 8.5
Details: 0.36M Sodium Acetate, 0.1M TRIS, 30% PEG 4000, pH 8.5, EVAPORATION, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.9782 / Wavelength: 0.9782, 0.9783, 0.9789, 0.9611
DetectorType: BRANDEIS / Detector: CCD / Date: Jun 4, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DIAMONDSINGLE WAVELENGTHMx-ray1
2DIAMONDMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97821
20.97831
30.97891
40.96111
ReflectionResolution: 2→30 Å / Num. obs: 25309 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 13.7 Å2 / Rsym value: 0.085
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.2 % / Rsym value: 0.705 / % possible all: 98.5

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Processing

Software
NameVersionClassification
DENZO1.97data reduction
SCALEPACK1.97data scaling
SOLVEphasing
PHASESphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2→8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1162581.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.239 1966 9.8 %RANDOM
Rwork0.216 ---
obs0.216 20158 81.4 %-
all-22124 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 73.4476 Å2 / ksol: 0.577852 e/Å3
Displacement parametersBiso mean: 35.6 Å2
Baniso -1Baniso -2Baniso -3
1-12.23 Å20 Å20 Å2
2---5.12 Å20 Å2
3----7.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1034 0 0 120 1154
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d14.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.63
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.12 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.239 202 9.5 %
Rwork0.228 1922 -
obs--52.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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