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- PDB-5c9n: Crystal structure of GEMC1 coiled-coil domain -

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Basic information

Entry
Database: PDB / ID: 5c9n
TitleCrystal structure of GEMC1 coiled-coil domain
ComponentsGeminin coiled-coil domain-containing protein 1
KeywordsCELL CYCLE / Geminin Idas coiled coil DNA replication license
Function / homology
Function and homology information


multi-ciliated epithelial cell differentiation / cerebrospinal fluid circulation / regulation of DNA-templated DNA replication initiation / seminiferous tubule development / negative regulation of cell cycle / cilium assembly / single fertilization / multicellular organism growth / spermatogenesis / DNA replication ...multi-ciliated epithelial cell differentiation / cerebrospinal fluid circulation / regulation of DNA-templated DNA replication initiation / seminiferous tubule development / negative regulation of cell cycle / cilium assembly / single fertilization / multicellular organism growth / spermatogenesis / DNA replication / chromatin binding / extracellular region / nucleus
Similarity search - Function
Geminin coiled-coil domain-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCaillat, C. / Perrakis, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: The structure of the GemC1 coiled coil and its interaction with the Geminin family of coiled-coil proteins.
Authors: Caillat, C. / Fish, A. / Pefani, D.E. / Taraviras, S. / Lygerou, Z. / Perrakis, A.
History
DepositionJun 28, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Geminin coiled-coil domain-containing protein 1
B: Geminin coiled-coil domain-containing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3614
Polymers20,1242
Non-polymers2362
Water66737
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-34 kcal/mol
Surface area9830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.035, 70.574, 83.055
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 coiled-coil domain-containing protein 1


Mass: 10062.223 Da / Num. of mol.: 2 / Fragment: UNP residues 64-148 / Mutation: L123E, L130E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GMNC, GEMC1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A6NCL1
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.64 Å3/Da / Density % sol: 66.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Hepes buffer pH 7.5, 7% Ethanol, 10% 2-Methyl-2,4-pentanediol (MPD) 0.01 M Ethylene-diamine-tetra-acetic acid disodium salt dihydrate.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.2→53.8 Å / Num. obs: 15376 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.871 / Mean I/σ(I) obs: 1.5 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UII

1uii


Resolution: 2.2→53.78 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.945 / SU B: 11.959 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24876 768 5 %RANDOM
Rwork0.22254 ---
obs0.22385 14601 99.16 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.241 Å2
Baniso -1Baniso -2Baniso -3
1--1.61 Å20 Å20 Å2
2--1.49 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.2→53.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1041 0 16 37 1094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191185
X-RAY DIFFRACTIONr_bond_other_d0.0010.021139
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.9861612
X-RAY DIFFRACTIONr_angle_other_deg0.87532641
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4065150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.02726.17668
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.51115242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.476158
X-RAY DIFFRACTIONr_chiral_restr0.0730.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021400
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02268
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
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_it1.5613.886561
X-RAY DIFFRACTIONr_mcbond_other1.563.878560
X-RAY DIFFRACTIONr_mcangle_it2.6985.783718
X-RAY DIFFRACTIONr_mcangle_other2.6965.792719
X-RAY DIFFRACTIONr_scbond_it1.6994.167624
X-RAY DIFFRACTIONr_scbond_other1.6984.175625
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8696.158893
X-RAY DIFFRACTIONr_long_range_B_refined6.1529.8471412
X-RAY DIFFRACTIONr_long_range_B_other6.14829.8891413
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 58 -
Rwork0.348 1069 -
obs--99.82 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.27510.3574-0.75877.9167-11.504917.49440.0713-0.0398-0.02460.141-0.07820.0053-0.11370.13510.00690.0632-0.029-0.01910.06570.04570.032229.78333.03924.849
20.23180.0090.101519.276-13.376210.11170.092-0.052-0.01870.1482-0.01010.1473-0.04950.1094-0.0820.0381-0.0087-0.00460.14350.02310.005533.15932.38322.224
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A69 - 132
2X-RAY DIFFRACTION2B69 - 129

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