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- PDB-6ewl: Danio rerio CEP120 first C2 domain (C2A) -

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Basic information

Entry
Database: PDB / ID: 6ewl
TitleDanio rerio CEP120 first C2 domain (C2A)
ComponentsCentrosomal protein 120
KeywordsCYTOSOLIC PROTEIN / Centriole Centrosome Basal body Cilia
Function / homologyC2 domain / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
Authorsvan Breugel, M. / al-Jassar, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UP_1201/3 United Kingdom
CitationJournal: Cell Rep / Year: 2018
Title: Disease-Associated Mutations in CEP120 Destabilize the Protein and Impair Ciliogenesis.
Authors: Joseph, N. / Al-Jassar, C. / Johnson, C.M. / Andreeva, A. / Barnabas, D.D. / Freund, S.M.V. / Gergely, F. / van Breugel, M.
History
DepositionNov 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Centrosomal protein 120


Theoretical massNumber of molelcules
Total (without water)15,9251
Polymers15,9251
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Monomer in solution as inferred from SEC-MALS experiments.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.459, 53.440, 74.659
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 120


Mass: 15925.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: cep120 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: A0A0G2KI14
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 1.97 Å3/Da / Density % sol: 37.58 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES, pH 7.5 200 mM MgCl2 30 % (v/v) PEG-400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.4→31.46 Å / Num. obs: 25380 / % possible obs: 99.3 % / Redundancy: 5.9 % / Biso Wilson estimate: 15.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.022 / Rrim(I) all: 0.054 / Net I/σ(I): 14.1
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1.7 / Num. measured obs: 3587 / CC1/2: 0.533 / Rpim(I) all: 0.435 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: C2 domain homology model

Resolution: 1.4→30.603 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.11 / Phase error: 22.85
RfactorNum. reflection% reflection
Rfree0.2021 2426 5.1 %
Rwork0.1625 --
obs0.1647 47584 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→30.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1102 0 0 154 1256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121202
X-RAY DIFFRACTIONf_angle_d1.2221638
X-RAY DIFFRACTIONf_dihedral_angle_d21.204478
X-RAY DIFFRACTIONf_chiral_restr0.108189
X-RAY DIFFRACTIONf_plane_restr0.008209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.42860.38511120.29922656X-RAY DIFFRACTION97
1.4286-1.45970.37651440.28222617X-RAY DIFFRACTION99
1.4597-1.49360.30151390.26742583X-RAY DIFFRACTION96
1.4936-1.5310.25031200.22632692X-RAY DIFFRACTION99
1.531-1.57240.2411300.20462677X-RAY DIFFRACTION99
1.5724-1.61860.22251620.17932638X-RAY DIFFRACTION100
1.6186-1.67090.25661430.18272649X-RAY DIFFRACTION99
1.6709-1.73060.22271240.1772688X-RAY DIFFRACTION100
1.7306-1.79990.24831610.15862636X-RAY DIFFRACTION99
1.7999-1.88180.21811380.14472669X-RAY DIFFRACTION100
1.8818-1.98090.18151540.142670X-RAY DIFFRACTION100
1.9809-2.1050.19671540.14152649X-RAY DIFFRACTION100
2.105-2.26750.18721660.1462642X-RAY DIFFRACTION100
2.2675-2.49560.20971700.16092648X-RAY DIFFRACTION100
2.4956-2.85650.23381320.17672713X-RAY DIFFRACTION100
2.8565-3.5980.17581420.15312650X-RAY DIFFRACTION100
3.598-30.610.17081350.15042681X-RAY DIFFRACTION100

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