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- PDB-4icw: N-terminal C2 domain of human CEP120 -

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Basic information

Entry
Database: PDB / ID: 4icw
TitleN-terminal C2 domain of human CEP120
ComponentsCentrosomal protein of 120 kDa
KeywordsTRANSPORT PROTEIN / C2 domain / lipid binding
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 ...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 / cytoplasm
Similarity search - Function
Domain of unknown function DUF3668 / Centrosomal protein of 120kDa-like / Cep120 protein / C2 domain / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Centrosomal protein of 120 kDa
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJanowski, R. / Guarin, N. / Coll, M.
CitationJournal: To be Published
Title: N-terminal C2 domain tandem of human CEP120 shows lipid binding properties
Authors: Janowski, R. / Guarin, N. / Speroni, S. / Serrano, L. / Coll, M.
History
DepositionDec 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Centrosomal protein of 120 kDa


Theoretical massNumber of molelcules
Total (without water)19,4071
Polymers19,4071
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.320, 48.880, 66.070
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 Centrosomal protein of 120 kDa / Cep120 / Coiled-coil domain-containing protein 100


Mass: 19407.268 Da / Num. of mol.: 1 / Fragment: C2 domain, UNP residues 1-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEP120, CCDC100 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q8N960
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / 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

Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 25% (v/w) PEG 3000 , pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9726 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9726 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 6902 / Num. obs: 6902 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 58.8 Å2 / Rmerge(I) obs: 0.029 / Net I/σ(I): 25.8
Reflection shellResolution: 2.2→2.26 Å / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 3.06 / % possible all: 98.6

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Processing

SoftwareName: REFMAC / Version: 5.5.0102 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.953 / SU B: 18.797 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.365 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23207 326 4.7 %RANDOM
Rwork0.21002 ---
all0.21105 6575 --
obs0.21105 6575 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 84.758 Å2
Baniso -1Baniso -2Baniso -3
1--2.84 Å20 Å20 Å2
2--5.84 Å20 Å2
3----2.99 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1060 0 0 13 1073
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221176
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.9661606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.015147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.17124.90955
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.29915220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.824156
X-RAY DIFFRACTIONr_chiral_restr0.0920.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021883
X-RAY DIFFRACTIONr_mcbond_it0.4961.5709
X-RAY DIFFRACTIONr_mcangle_it0.9862.51166
X-RAY DIFFRACTIONr_scbond_it2.6385467
X-RAY DIFFRACTIONr_scangle_it4.53910435
LS refinement shellResolution: 2.2→2.318 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.306 49 -
Rwork0.283 936 -
obs--98.9 %
Refinement TLS params.Method: refined / Origin x: 11.3244 Å / Origin y: -8.0511 Å / Origin z: -13.9524 Å
111213212223313233
T0.1909 Å2-0.0042 Å20.0183 Å2-0.0967 Å20.0401 Å2--0.1512 Å2
L5.4609 °20.6935 °2-2.3387 °2-2.9161 °2-0.9795 °2--4.6056 °2
S0.0246 Å °0.5115 Å °0.2178 Å °-0.4633 Å °0.008 Å °-0.1815 Å °-0.0186 Å °0.087 Å °-0.0326 Å °

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