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- PDB-5lpi: Structure of the zinc finger array of Cep104 -

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Basic information

Entry
Database: PDB / ID: 5lpi
TitleStructure of the zinc finger array of Cep104
ComponentsCentrosomal protein of 104 kDa
KeywordsCELL CYCLE / Zinc finger array / Cep104 / Basal body / Centriole Cilia
Function / homology
Function and homology information


centriole / spindle pole / cilium / centrosome / cytoplasm
Similarity search - Function
: / : / : / Centrosomal protein CEP104, N-terminal domain / Centrosomal protein CEP104, ZnF / Centrosomal protein CEP104-like, TOG domain / TOG domain / TOG / Galactose-binding-like domain superfamily / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Centrosomal protein of 104 kDa
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.8 Å
Authorsvan Breugel, M. / Yu, M. / al Jassar, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UP_1201/3 United Kingdom
CitationJournal: Structure / Year: 2017
Title: The Ciliopathy-Associated Cep104 Protein Interacts with Tubulin and Nek1 Kinase.
Authors: Al-Jassar, C. / Andreeva, A. / Barnabas, D.D. / McLaughlin, S.H. / Johnson, C.M. / Yu, M. / van Breugel, M.
History
DepositionAug 13, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Sep 13, 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
D: Centrosomal protein of 104 kDa
C: Centrosomal protein of 104 kDa
A: Centrosomal protein of 104 kDa
B: Centrosomal protein of 104 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,23820
Polymers62,1914
Non-polymers1,04716
Water6,972387
1
D: Centrosomal protein of 104 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8095
Polymers15,5481
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Centrosomal protein of 104 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8095
Polymers15,5481
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Centrosomal protein of 104 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8095
Polymers15,5481
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Centrosomal protein of 104 kDa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8095
Polymers15,5481
Non-polymers2624
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.149, 80.320, 118.130
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 104 kDa / Cep104


Mass: 15547.859 Da / Num. of mol.: 4 / Fragment: UNP residues 746-875
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEP104, KIAA0562 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: O60308
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.83 Å3/Da / Density % sol: 56.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10 % PEG 4K 20% Glycerol 30 mM CaCl2 30 mM MgCl2 0.1M MES/imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→30.31 Å / Num. obs: 66109 / % possible obs: 100 % / Redundancy: 7.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Net I/σ(I): 13.6
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 7 % / Mean I/σ(I) obs: 1.3 / CC1/2: 0.444 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
SHELXDEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.246 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0.03 / Phase error: 24.93
RfactorNum. reflection% reflection
Rfree0.2294 6109 4.84 %
Rwork0.1919 --
obs0.1936 66016 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→29.246 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4271 0 16 387 4674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074401
X-RAY DIFFRACTIONf_angle_d0.8095919
X-RAY DIFFRACTIONf_dihedral_angle_d11.5032687
X-RAY DIFFRACTIONf_chiral_restr0.052603
X-RAY DIFFRACTIONf_plane_restr0.005774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82040.42471940.38384052X-RAY DIFFRACTION100
1.8204-1.84190.40112070.36133945X-RAY DIFFRACTION100
1.8419-1.86430.35791790.34634070X-RAY DIFFRACTION100
1.8643-1.88790.33242060.31483997X-RAY DIFFRACTION100
1.8879-1.91280.33082050.30394033X-RAY DIFFRACTION100
1.9128-1.93890.33161610.29774039X-RAY DIFFRACTION100
1.9389-1.96660.35341750.29274027X-RAY DIFFRACTION100
1.9666-1.9960.30092230.26383954X-RAY DIFFRACTION100
1.996-2.02720.30162010.25933990X-RAY DIFFRACTION100
2.0272-2.06040.26741740.25864149X-RAY DIFFRACTION100
2.0604-2.09590.26662090.24923912X-RAY DIFFRACTION100
2.0959-2.1340.23021900.2394042X-RAY DIFFRACTION100
2.134-2.17510.25812040.22394017X-RAY DIFFRACTION100
2.1751-2.21940.26732230.21913958X-RAY DIFFRACTION100
2.2194-2.26770.24392240.2144020X-RAY DIFFRACTION100
2.2677-2.32040.2532010.20484010X-RAY DIFFRACTION100
2.3204-2.37840.21182070.20044005X-RAY DIFFRACTION100
2.3784-2.44270.2411990.19593990X-RAY DIFFRACTION100
2.4427-2.51450.232180.20024004X-RAY DIFFRACTION100
2.5145-2.59560.24432570.19423978X-RAY DIFFRACTION100
2.5956-2.68830.24752500.19593924X-RAY DIFFRACTION100
2.6883-2.79590.20942140.18573981X-RAY DIFFRACTION100
2.7959-2.9230.24072070.19134001X-RAY DIFFRACTION100
2.923-3.0770.25071660.19444052X-RAY DIFFRACTION100
3.077-3.26950.2772060.20194006X-RAY DIFFRACTION100
3.2695-3.52160.22072380.1743973X-RAY DIFFRACTION100
3.5216-3.87530.18382060.16384006X-RAY DIFFRACTION100
3.8753-4.43440.18961820.14454009X-RAY DIFFRACTION100
4.4344-5.58050.16991620.14844058X-RAY DIFFRACTION100
5.5805-29.24940.19272210.15783955X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 21.7878 Å / Origin y: 82.1028 Å / Origin z: 51.7349 Å
111213212223313233
T0.1893 Å20.019 Å20.0095 Å2-0.1576 Å2-0.0127 Å2--0.1492 Å2
L1.0786 °2-0.2493 °2-0.1742 °2-1.0104 °20.213 °2--0.5208 °2
S-0.0083 Å °0.0387 Å °-0.0155 Å °0.0524 Å °0.0077 Å °-0.0023 Å °-0.0172 Å °-0.0073 Å °-0.0007 Å °
Refinement TLS groupSelection details: all

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