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- PDB-4bry: The Idas:Geminin heterodimeric parallel coiled-coil -

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Basic information

Entry
Database: PDB / ID: 4bry
TitleThe Idas:Geminin heterodimeric parallel coiled-coil
Components
  • GEMININ
  • MULTICILIN
KeywordsCELL CYCLE / DNA REPLICATION LICENSING
Function / homology
Function and homology information


multi-ciliated epithelial cell differentiation / DNA replication preinitiation complex assembly / centriole assembly / Switching of origins to a post-replicative state / regulation of cilium assembly / negative regulation of DNA-templated DNA replication / motile cilium assembly / regulation of DNA-templated DNA replication initiation / positive regulation of chromatin binding / negative regulation of DNA replication ...multi-ciliated epithelial cell differentiation / DNA replication preinitiation complex assembly / centriole assembly / Switching of origins to a post-replicative state / regulation of cilium assembly / negative regulation of DNA-templated DNA replication / motile cilium assembly / regulation of DNA-templated DNA replication initiation / positive regulation of chromatin binding / negative regulation of DNA replication / regulation of DNA replication / negative regulation of cell cycle / cilium assembly / 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 / nuclear body / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Geminin coiled-coil domain / Geminin/Multicilin / Geminin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Multicilin / Geminin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsCaillat, C. / Perrakis, A.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The Geminin and Idas Coiled Coils Preferentially Form a Heterodimer that Inhibits Geminin Function in DNA Replication Licensing
Authors: Caillate, C. / Pefani, E.D. / Gillespie, P.J. / Taraviras, S. / Blow, J.J. / Lygerou, Z. / Perrakis, A.
History
DepositionJun 6, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: GEMININ
B: MULTICILIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3406
Polymers17,7622
Non-polymers5784
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-26 kcal/mol
Surface area11770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.799, 117.799, 103.462
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein GEMININ


Mass: 9376.613 Da / Num. of mol.: 1 / Fragment: COILED-COIL, RESIDUES 83-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET-NKI-LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O75496
#2: Protein MULTICILIN / MULTICILIATE DIFFERENTIATION AND DNA SYNTHESIS-ASSOCIATED CELL CYCLE PROTEIN / PROTEIN IDAS / IDAS


Mass: 8385.453 Da / Num. of mol.: 1 / Fragment: COILED-COIL, RESIDUES 173-245
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: D6RGH6
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4

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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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M SPG PH 7.5, 10 % ISOPROPANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.992
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.992 Å / Relative weight: 1
ReflectionResolution: 2.89→46.95 Å / Num. obs: 8415 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 81.3 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.8
Reflection shellResolution: 2.89→3.05 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2.3 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UII

1uii


Resolution: 2.89→46.946 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.941 / SU B: 21.734 / SU ML: 0.191 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.373 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 633 7.58 %RANDOM
Rwork0.2026 ---
obs0.204 8398 99.55 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 53.113 Å2
Baniso -1Baniso -2Baniso -3
1--0.693 Å20 Å20 Å2
2---0.693 Å20 Å2
3---1.386 Å2
Refinement stepCycle: LAST / Resolution: 2.89→46.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1139 0 36 0 1175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191185
X-RAY DIFFRACTIONr_bond_other_d0.0050.02847
X-RAY DIFFRACTIONr_angle_refined_deg2.2961.9921582
X-RAY DIFFRACTIONr_angle_other_deg1.05432077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9995136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.81225.87363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.66415238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.328158
X-RAY DIFFRACTIONr_chiral_restr0.1020.2170
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021255
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02201
X-RAY DIFFRACTIONr_nbd_refined0.2960.2297
X-RAY DIFFRACTIONr_nbd_other0.2180.223
X-RAY DIFFRACTIONr_nbtor_refined0.2140.2530
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0930.228
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6064.1621183
X-RAY DIFFRACTIONr_mcbond_other1.064.332846
X-RAY DIFFRACTIONr_mcangle_it7.3856.0871582
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it12.33512.41445
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.21818.019894
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.89→2.965 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 45 -
Rwork0.333 491 -
obs--98.711 %
Refinement TLS params.Method: refined / Origin x: 6.7041 Å / Origin y: 25.065 Å / Origin z: -18.7028 Å
111213212223313233
T0.106 Å20.0206 Å20.013 Å2-0.2831 Å20.0421 Å2--0.0582 Å2
L9.9135 °2-0.2122 °2-1.2187 °2-0.3389 °20.1896 °2--0.3319 °2
S0.2783 Å °0.1578 Å °0.0046 Å °-0.031 Å °-0.1836 Å °-0.0527 Å °-0.0933 Å °-0.098 Å °-0.0946 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A92 - 160
2X-RAY DIFFRACTION1B176 - 244

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