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- PDB-6ewg: Oreochromis niloticus CEP120 second C2 domain (C2B) -

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Basic information

Entry
Database: PDB / ID: 6ewg
TitleOreochromis niloticus CEP120 second C2 domain (C2B)
ComponentsCentrosomal protein 120Centrosome
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 / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
Authorsvan Breugel, 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 1.2Jan 17, 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

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Assembly

Deposited unit
A: Centrosomal protein 120


Theoretical massNumber of molelcules
Total (without water)20,9951
Polymers20,9951
Non-polymers00
Water2,558142
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 area10520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.389, 67.488, 89.119
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 / Centrosome


Mass: 20994.924 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 / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 52.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 Na-MES pH ~6.5 30% PEG 400 / PH range: pH gradient around pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.6→89.12 Å / Num. obs: 29804 / % possible obs: 100 % / Redundancy: 12.7 % / Biso Wilson estimate: 28.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.018 / Rrim(I) all: 0.065 / Net I/σ(I): 15.5
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 13.2 % / Mean I/σ(I) obs: 1.6 / Num. measured obs: 29602 / Num. unique obs: 1461 / CC1/2: 0.812 / Rpim(I) all: 0.536 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EWH

6ewh


Resolution: 1.6→37.186 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.77
RfactorNum. reflection% reflection
Rfree0.2028 2789 5.01 %
Rwork0.1854 --
obs0.1863 55679 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→37.186 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1386 0 0 142 1528
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051480
X-RAY DIFFRACTIONf_angle_d0.8112034
X-RAY DIFFRACTIONf_dihedral_angle_d9.681934
X-RAY DIFFRACTIONf_chiral_restr0.054248
X-RAY DIFFRACTIONf_plane_restr0.005263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62760.39051560.32442613X-RAY DIFFRACTION99
1.6276-1.65720.36251410.29422647X-RAY DIFFRACTION99
1.6572-1.68910.2821380.29632597X-RAY DIFFRACTION99
1.6891-1.72360.3311430.28222611X-RAY DIFFRACTION99
1.7236-1.7610.32141480.27432580X-RAY DIFFRACTION99
1.761-1.8020.27461360.25342683X-RAY DIFFRACTION99
1.802-1.84710.28241400.22562623X-RAY DIFFRACTION100
1.8471-1.8970.22231290.22192647X-RAY DIFFRACTION99
1.897-1.95280.24761360.212651X-RAY DIFFRACTION100
1.9528-2.01580.22471560.20522668X-RAY DIFFRACTION100
2.0158-2.08790.26471600.20752596X-RAY DIFFRACTION100
2.0879-2.17150.21181240.20892700X-RAY DIFFRACTION100
2.1715-2.27030.24571450.20352665X-RAY DIFFRACTION100
2.2703-2.390.2211570.20692618X-RAY DIFFRACTION100
2.39-2.53970.26021350.20262652X-RAY DIFFRACTION100
2.5397-2.73570.20071230.19732684X-RAY DIFFRACTION100
2.7357-3.01090.21741310.19822664X-RAY DIFFRACTION100
3.0109-3.44630.18051310.17892656X-RAY DIFFRACTION100
3.4463-4.34090.16521200.15392685X-RAY DIFFRACTION100
4.3409-37.19560.161400.15312650X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -4.8255 Å / Origin y: 7.848 Å / Origin z: -14.9286 Å
111213212223313233
T0.2107 Å2-0.0368 Å2-0.0184 Å2-0.1817 Å20.0034 Å2--0.1411 Å2
L4.5426 °2-2.0729 °2-1.2575 °2-2.9481 °20.9017 °2--1.4975 °2
S-0.0203 Å °-0.0087 Å °-0.0704 Å °0.1063 Å °0.037 Å °0.0038 Å °0.109 Å °-0.0819 Å °-0.0371 Å °
Refinement TLS groupSelection details: all

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