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

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Basic information

Entry
Database: PDB / ID: 4icx
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 / SAD / Resolution: 2.7 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 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Centrosomal protein of 120 kDa
B: Centrosomal protein of 120 kDa
C: Centrosomal protein of 120 kDa


Theoretical massNumber of molelcules
Total (without water)58,6443
Polymers58,6443
Non-polymers00
Water1,04558
1
A: Centrosomal protein of 120 kDa


Theoretical massNumber of molelcules
Total (without water)19,5481
Polymers19,5481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Centrosomal protein of 120 kDa


Theoretical massNumber of molelcules
Total (without water)19,5481
Polymers19,5481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Centrosomal protein of 120 kDa


Theoretical massNumber of molelcules
Total (without water)19,5481
Polymers19,5481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.280, 117.390, 134.840
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: 19547.953 Da / Num. of mol.: 3 / 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.: 58 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 200 mM sodium chloride and 23% (v/w) PEG 3350 , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 24, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 49.4 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 16.6
Reflection shellResolution: 2.7→2.77 Å / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 3.2 / % possible all: 77.7

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Processing

Software
NameVersionClassification
DNAdata collection
Auto-Rickshawphasing
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.895 / SU B: 25.327 / SU ML: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.519 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25265 915 5.2 %RANDOM
Rwork0.19586 ---
all0.1987 16770 --
obs0.1987 16770 96.67 %-
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: 72.998 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å20 Å20 Å2
2--4.01 Å20 Å2
3----2.24 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3208 0 0 58 3266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223304
X-RAY DIFFRACTIONr_angle_refined_deg1.0631.9654483
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9615399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.66324.679156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.17715618
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7721519
X-RAY DIFFRACTIONr_chiral_restr0.0730.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212454
X-RAY DIFFRACTIONr_mcbond_it0.4221.51991
X-RAY DIFFRACTIONr_mcangle_it0.9092.53252
X-RAY DIFFRACTIONr_scbond_it2.48951313
X-RAY DIFFRACTIONr_scangle_it4.37101227
LS refinement shellResolution: 2.7→2.845 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.282 129 -
Rwork0.239 1930 -
obs--79.87 %
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)
12.8028-0.6839-0.96622.54982.46555.1150.03580.0701-0.2152-0.02440.1493-0.13970.32470.1486-0.18510.04780.009-0.0210.0487-0.06570.095516.44317.0599124.8285
25.5771-1.2597-3.01533.38951.90685.0312-0.14820.1943-0.3105-0.19220.0348-0.14410.2611-0.05990.11330.0469-0.00860.02260.0095-0.01860.042816.288634.6367120.6105
32.02221.7560.19410.08562.93041.85130.0580.0792-0.0415-1.13890.3474-0.6199-0.60960.2791-0.40540.4911-0.07530.21120.2464-0.22520.249228.57614.184995.4501
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 135
2X-RAY DIFFRACTION2B6 - 135
3X-RAY DIFFRACTION3C6 - 135

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