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- PDB-5jo8: CEP104 TOG domain -

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Basic information

Entry
Database: PDB / ID: 5jo8
TitleCEP104 TOG domain
ComponentsCEP104
KeywordsSTRUCTURAL PROTEIN / centriolar protein / TOG domain / CEP104 / microtubule binder
Function / homologyTOG domain / TOG / Galactose-binding-like domain superfamily / Armadillo-like helical / Armadillo-type fold / TOG domain-containing protein
Function and homology information
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsRezabkova, L. / Kraatz, S.H.W.
Funding support Belgium, Germany, 2items
OrganizationGrant numberCountry
Marie Curie IEF Belgium
European Molecular Biology Organization Germany
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Biophysical and Structural Characterization of the Centriolar Protein Cep104 Interaction Network.
Authors: Rezabkova, L. / Kraatz, S.H. / Akhmanova, A. / Steinmetz, M.O. / Kammerer, R.A.
History
DepositionMay 2, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 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

Downloads & links

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Assembly

Deposited unit
A: CEP104


Theoretical massNumber of molelcules
Total (without water)31,3821
Polymers31,3821
Non-polymers00
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.360, 57.220, 102.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-515-

HOH

21A-538-

HOH

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Components

#1: Protein CEP104


Mass: 31381.744 Da / Num. of mol.: 1 / Fragment: TOG domain, UNP residues 429-686
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: CEP104 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E1C2W2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 1500, 0.1 M MMT pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0, 0.96
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.961
ReflectionResolution: 1.4→50 Å / Num. obs: 55668 / % possible obs: 97 % / Redundancy: 16.4 % / CC1/2: 1 / Rmerge(I) obs: 0.065 / Net I/σ(I): 19.02
Reflection shellResolution: 1.4→1.44 Å / Redundancy: 16.5 % / Rmerge(I) obs: 2.76 / Mean I/σ(I) obs: 1.05 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1965refinement
XDSdata reduction
XSCALEdata scaling
AutoSolphasing
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→43.772 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.12
RfactorNum. reflection% reflection
Rfree0.2383 1982 3.57 %
Rwork0.2186 --
obs0.2192 55550 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→43.772 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2027 0 0 248 2275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062118
X-RAY DIFFRACTIONf_angle_d12867
X-RAY DIFFRACTIONf_dihedral_angle_d11.465816
X-RAY DIFFRACTIONf_chiral_restr0.069334
X-RAY DIFFRACTIONf_plane_restr0.005358
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.4350.4181420.40683847X-RAY DIFFRACTION100
1.435-1.47380.39351430.37173867X-RAY DIFFRACTION100
1.4738-1.51720.32471430.32063846X-RAY DIFFRACTION99
1.5172-1.56610.31221410.30233778X-RAY DIFFRACTION97
1.5661-1.62210.31791280.30433464X-RAY DIFFRACTION89
1.6221-1.68710.2891450.23813886X-RAY DIFFRACTION100
1.6871-1.76380.28051450.22583881X-RAY DIFFRACTION100
1.7638-1.85680.29761450.22583927X-RAY DIFFRACTION100
1.8568-1.97320.31631420.23343846X-RAY DIFFRACTION98
1.9732-2.12550.24651450.20413880X-RAY DIFFRACTION99
2.1255-2.33940.24851460.19313955X-RAY DIFFRACTION100
2.3394-2.67790.22111390.23783768X-RAY DIFFRACTION95
2.6779-3.37370.21291380.21633783X-RAY DIFFRACTION94
3.3737-43.79340.19681400.18763840X-RAY DIFFRACTION92

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