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- PDB-6flk: Crystal structure of Cep120 C2C domain -

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Basic information

Entry
Database: PDB / ID: 6flk
TitleCrystal structure of Cep120 C2C domain
ComponentsCep120
KeywordsSTRUCTURAL PROTEIN / Centriole / microtubule / Cep120 / C2 domain
Function / homology
Function and homology information


interkinetic nuclear migration / positive regulation of centriole elongation / positive regulation of establishment of protein localization / positive regulation of centrosome duplication / astral microtubule organization / positive regulation of cilium assembly / centrosome cycle / neurogenesis / centriole / cerebral cortex development / centrosome
Similarity search - Function
Domain of unknown function DUF3668 / Centrosomal protein of 120kDa-like / Cep120 protein / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
Centrosomal protein of 120 kDa
Similarity search - Component
Biological specieshomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsSharma, A. / Gerard, S.F. / Olieric, N. / Steinmetz, M.O.
CitationJournal: J. Struct. Biol. / Year: 2018
Title: Cep120 promotes microtubule formation through a unique tubulin binding C2 domain.
Authors: Sharma, A. / Gerard, S.F. / Olieric, N. / Steinmetz, M.O.
History
DepositionJan 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 8, 2024Group: 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: Cep120
B: Cep120


Theoretical massNumber of molelcules
Total (without water)37,0752
Polymers37,0752
Non-polymers00
Water6,918384
1
A: Cep120


Theoretical massNumber of molelcules
Total (without water)18,5371
Polymers18,5371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cep120


Theoretical massNumber of molelcules
Total (without water)18,5371
Polymers18,5371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.400, 40.954, 69.132
Angle α, β, γ (deg.)102.47, 98.07, 89.92
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Cep120


Mass: 18537.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N960
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.39 Å3/Da / Density % sol: 48.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.03M magnesium chloride hexahydrate; 0.03M calcium chloride dehydrate, 0.1M Tris(Base)/BICINE pH 8.5, 20% v/v Ethylene glycol and 10 % w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→39.97 Å / Num. obs: 42539 / % possible obs: 93.83 % / Redundancy: 1.8 % / Biso Wilson estimate: 15.125252799 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.0819 / Rrim(I) all: 0.1158 / Net I/σ(I): 6.87
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.6926 / Mean I/σ(I) obs: 1.08 / Num. unique obs: 3744 / CC1/2: 0.439 / Rrim(I) all: 0.9794 / % possible all: 83.09

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Processing

Software
NameVersionClassification
PHENIX(dev_2863: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→39.97 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.2 / Phase error: 27.61
RfactorNum. reflection% reflection
Rfree0.2464 3437 4.99 %
Rwork0.1974 --
obs0.1998 42534 75.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→39.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2484 0 0 384 2868
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0222635
X-RAY DIFFRACTIONf_angle_d2.3943588
X-RAY DIFFRACTIONf_dihedral_angle_d22.307968
X-RAY DIFFRACTIONf_chiral_restr0.123395
X-RAY DIFFRACTIONf_plane_restr0.013458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62190.39671040.31511895X-RAY DIFFRACTION55
1.6219-1.64510.36451110.3142180X-RAY DIFFRACTION63
1.6451-1.66970.3531220.30642386X-RAY DIFFRACTION69
1.6697-1.69570.33241260.29452405X-RAY DIFFRACTION70
1.6957-1.72350.33981380.28032496X-RAY DIFFRACTION73
1.7235-1.75330.32111230.27552494X-RAY DIFFRACTION74
1.7533-1.78510.32261390.28152610X-RAY DIFFRACTION73
1.7851-1.81950.33411360.272546X-RAY DIFFRACTION76
1.8195-1.85660.3311380.26292642X-RAY DIFFRACTION76
1.8566-1.8970.29521320.26252614X-RAY DIFFRACTION76
1.897-1.94110.29481380.22662588X-RAY DIFFRACTION75
1.9411-1.98970.27741340.21232450X-RAY DIFFRACTION72
1.9897-2.04350.26531350.20192537X-RAY DIFFRACTION74
2.0435-2.10360.23761460.19442648X-RAY DIFFRACTION77
2.1036-2.17150.25821470.18282783X-RAY DIFFRACTION80
2.1715-2.24910.21811520.18352858X-RAY DIFFRACTION83
2.2491-2.33910.23191410.17932735X-RAY DIFFRACTION80
2.3391-2.44560.22631430.18292828X-RAY DIFFRACTION81
2.4456-2.57450.27911490.18062751X-RAY DIFFRACTION80
2.5745-2.73570.23011300.18372682X-RAY DIFFRACTION78
2.7357-2.94690.19391420.17032588X-RAY DIFFRACTION75
2.9469-3.24330.2351550.16712864X-RAY DIFFRACTION84
3.2433-3.71240.2111510.15842928X-RAY DIFFRACTION86
3.7124-4.6760.16551500.15332938X-RAY DIFFRACTION85
4.676-39.98270.26861550.22082933X-RAY DIFFRACTION85

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