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- PDB-6ewh: Oreochromis niloticus CEP120 second C2 domain (C2B) G307S mutant -

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Basic information

Entry
Database: PDB / ID: 6ewh
TitleOreochromis niloticus CEP120 second C2 domain (C2B) G307S mutant
ComponentsCentrosomal protein 120
KeywordsCYTOSOLIC PROTEIN / Centriole Centrosome Basal body Cilia
Function / homologyDomain of unknown function DUF3668 / Centrosomal protein of 120kDa-like / Cep120 protein / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / Centrosomal protein 120
Function and homology information
Biological speciesOreochromis niloticus (Nile tilapia)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
Authorsvan Breugel, M. / al-Jassar, C. / Yu, M.
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 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

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Assembly

Deposited unit
A: Centrosomal protein 120


Theoretical massNumber of molelcules
Total (without water)21,0251
Polymers21,0251
Non-polymers00
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Monomer in solution based on SEC-MALS experiments
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.449, 67.250, 89.379
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: 21024.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oreochromis niloticus (Nile tilapia) / Gene: cep120 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: I3K8D3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.61 Å3/Da / Density % sol: 52.78 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.1 / Details: 100 mM Na-MES, pH 6.1 29 % (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: 1.5→31.47 Å / Num. obs: 36042 / % possible obs: 100 % / Redundancy: 6 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 17.2
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.5→30.17 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 24.16
RfactorNum. reflection% reflection
Rfree0.206 3394 5 %
Rwork0.184 --
obs0.185 35948 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→30.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1388 0 0 202 1590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051492
X-RAY DIFFRACTIONf_angle_d0.8292054
X-RAY DIFFRACTIONf_dihedral_angle_d15.015576
X-RAY DIFFRACTIONf_chiral_restr0.078252
X-RAY DIFFRACTIONf_plane_restr0.006266
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.52140.33731170.33082677X-RAY DIFFRACTION100
1.5214-1.54410.35111510.31852633X-RAY DIFFRACTION100
1.5441-1.56820.35611500.30382713X-RAY DIFFRACTION100
1.5682-1.5940.32271540.30522702X-RAY DIFFRACTION100
1.594-1.62140.28091550.27982648X-RAY DIFFRACTION100
1.6214-1.65090.32651250.26932709X-RAY DIFFRACTION100
1.6509-1.68270.25781580.26182650X-RAY DIFFRACTION100
1.6827-1.7170.26541400.25132713X-RAY DIFFRACTION100
1.717-1.75430.26061380.23572684X-RAY DIFFRACTION100
1.7543-1.79520.27811460.23492651X-RAY DIFFRACTION100
1.7952-1.840.3061400.22212711X-RAY DIFFRACTION100
1.84-1.88980.22821410.21182680X-RAY DIFFRACTION100
1.8898-1.94540.23911320.19712724X-RAY DIFFRACTION100
1.9454-2.00820.25641570.18822660X-RAY DIFFRACTION100
2.0082-2.07990.22561620.1982658X-RAY DIFFRACTION100
2.0799-2.16320.22811300.20232711X-RAY DIFFRACTION100
2.1632-2.26160.18951510.18992700X-RAY DIFFRACTION100
2.2616-2.38080.20531600.18912656X-RAY DIFFRACTION100
2.3808-2.52990.2611350.19362690X-RAY DIFFRACTION100
2.5299-2.72510.23621280.19272724X-RAY DIFFRACTION100
2.7251-2.99910.24511250.18582697X-RAY DIFFRACTION100
2.9991-3.43260.18271380.17492687X-RAY DIFFRACTION100
3.4326-4.32260.15971190.15312719X-RAY DIFFRACTION100
4.3226-30.1710.15361420.15172687X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -4.8736 Å / Origin y: 7.6894 Å / Origin z: -15.0564 Å
111213212223313233
T0.22 Å2-0.0251 Å20.0019 Å2-0.2152 Å2-0.0164 Å2--0.1877 Å2
L1.919 °2-0.573 °2-0.7547 °2-1.2596 °20.2242 °2--0.9106 °2
S-0.0459 Å °0.0989 Å °-0.0902 Å °0.0609 Å °0.0188 Å °0.0285 Å °0.1218 Å °-0.1321 Å °0 Å °
Refinement TLS groupSelection details: ALL

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