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- PDB-6hxy: Crystal structure of the head and coiled-coil domains of zebrafis... -

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Basic information

Entry
Database: PDB / ID: 6hxy
TitleCrystal structure of the head and coiled-coil domains of zebrafish CCDC61
ComponentsCoiled-coil domain-containing protein 61
KeywordsSTRUCTURAL PROTEIN / Centrosome / cilia / scaffold protein / proto-filament
Function / homology
Function and homology information


centriolar subdistal appendage / centriole assembly / cell projection organization / microtubule organizing center / centriolar satellite / mitotic spindle assembly / ciliary basal body / centrosome / identical protein binding / cytoplasm
Similarity search - Function
Centrosomal protein CCDC61
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsOchi, T. / van Breugel, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom) United Kingdom
CitationJournal: Structure / Year: 2020
Title: CCDC61/VFL3 Is a Paralog of SAS6 and Promotes Ciliary Functions.
Authors: Ochi, T. / Quarantotti, V. / Lin, H. / Jullien, J. / Rosa E Silva, I. / Boselli, F. / Barnabas, D.D. / Johnson, C.M. / McLaughlin, S.H. / Freund, S.M.V. / Blackford, A.N. / Kimata, Y. / ...Authors: Ochi, T. / Quarantotti, V. / Lin, H. / Jullien, J. / Rosa E Silva, I. / Boselli, F. / Barnabas, D.D. / Johnson, C.M. / McLaughlin, S.H. / Freund, S.M.V. / Blackford, A.N. / Kimata, Y. / Goldstein, R.E. / Jackson, S.P. / Blundell, T.L. / Dutcher, S.K. / Gergely, F. / van Breugel, M.
History
DepositionOct 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.2May 20, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jun 10, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.4Jan 24, 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: Coiled-coil domain-containing protein 61
B: Coiled-coil domain-containing protein 61


Theoretical massNumber of molelcules
Total (without water)39,0752
Polymers39,0752
Non-polymers00
Water48627
1
A: Coiled-coil domain-containing protein 61
B: Coiled-coil domain-containing protein 61

A: Coiled-coil domain-containing protein 61
B: Coiled-coil domain-containing protein 61


Theoretical massNumber of molelcules
Total (without water)78,1504
Polymers78,1504
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Unit cell
Length a, b, c (Å)93.088, 100.560, 135.759
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Coiled-coil domain-containing protein 61


Mass: 19537.479 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: ccdc61, zgc:153153 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q08CF3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 4.07 Å3/Da / Density % sol: 69.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 1 M LiCl, 100 mM Citric acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.9→68.31 Å / Num. obs: 14498 / % possible obs: 100 % / Redundancy: 5.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.051 / Rrim(I) all: 0.124 / Net I/σ(I): 9.4
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.849 / Mean I/σ(I) obs: 2 / Num. unique obs: 2302 / CC1/2: 0.84 / Rpim(I) all: 0.375 / Rrim(I) all: 0.93 / % possible all: 100

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Processing

Software
NameClassification
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HXV

6hxv


Resolution: 2.9→67.879 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.81
RfactorNum. reflection% reflection
Rfree0.2581 1454 10.06 %
Rwork0.1999 --
obs0.2057 14453 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 83.16 Å2
Refinement stepCycle: LAST / Resolution: 2.9→67.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2327 0 0 27 2354
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082383
X-RAY DIFFRACTIONf_angle_d1.2033239
X-RAY DIFFRACTIONf_dihedral_angle_d16.235872
X-RAY DIFFRACTIONf_chiral_restr0.053378
X-RAY DIFFRACTIONf_plane_restr0.008414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.00370.34881400.29731284X-RAY DIFFRACTION100
3.0037-3.1240.37281500.27891275X-RAY DIFFRACTION100
3.124-3.26620.34341370.24951283X-RAY DIFFRACTION100
3.2662-3.43840.36491520.22921285X-RAY DIFFRACTION100
3.4384-3.65380.24271360.21091289X-RAY DIFFRACTION100
3.6538-3.93590.25171380.18171291X-RAY DIFFRACTION100
3.9359-4.33190.18661510.15731299X-RAY DIFFRACTION100
4.3319-4.95860.21861460.14641294X-RAY DIFFRACTION100
4.9586-6.24660.2741480.20491330X-RAY DIFFRACTION100
6.2466-67.89810.25241560.21311369X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1121-0.02340.2320.2892-0.12150.38060.6583-0.05370.0821-0.14770.09980.0764-0.34190.06470.95620.6225-0.02520.56280.4129-0.00680.4876-35.2436-18.01120.8963
20.00390.0029-0.00460.00640.00270.00720.04220.045-0.0361-0.0393-0.03720.0066-0.02390.0172-01.0493-0.15760.31631.1622-0.15530.625-21.1456-18.1189-3.6221
30.2121-0.08120.0260.32790.0450.06660.2785-0.1565-0.05020.3317-0.48690.1016-0.0827-0.0807-0.22960.3399-0.07220.12970.3412-0.00360.3367-5.9703-6.5479-17.1046
40.00330.00030.00430.0065-0.0029-0.00080.03630.0137-0.02070.0995-0.04650.0301-0.1089-0.0742-00.799-0.11610.4250.90310.06890.8225-28.7311-14.0266-0.2209
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 3:144
2X-RAY DIFFRACTION2chain A and resseq 145:163
3X-RAY DIFFRACTION3chain B and resseq 2:144
4X-RAY DIFFRACTION4chain B and resseq 145:163

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