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- PDB-5i7c: Centrosomin-motif 2 (CM2) domain of Drosophila melanogaster Centr... -

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Basic information

Entry
Database: PDB / ID: 5i7c
TitleCentrosomin-motif 2 (CM2) domain of Drosophila melanogaster Centrosomin (Cnn)
ComponentsCentrosominCDK5RAP2
KeywordsSTRUCTURAL PROTEIN / Non-canonical-coiled-coil / Centrosome / PCM / Zinc-binding
Function / homology
Function and homology information


photoreceptor cell morphogenesis / regulation of Golgi organization / pole cell formation / asymmetric cell division / regulation of centriole-centriole cohesion / asymmetric neuroblast division / positive regulation of microtubule nucleation / embryonic cleavage / peripheral nervous system development / motile cilium ...photoreceptor cell morphogenesis / regulation of Golgi organization / pole cell formation / asymmetric cell division / regulation of centriole-centriole cohesion / asymmetric neuroblast division / positive regulation of microtubule nucleation / embryonic cleavage / peripheral nervous system development / motile cilium / centrosome cycle / midgut development / pericentriolar material / centriole replication / centriole / mitotic spindle organization / ciliary basal body / meiotic cell cycle / central nervous system development / spindle pole / molecular adaptor activity / centrosome / Golgi apparatus
Similarity search - Function
Centrosomin, N-terminal motif 1 / Centrosomin N-terminal motif 1
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.804 Å
AuthorsFeng, Z. / Cottee, M.A. / Johnson, S. / Lea, S.M.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust104575/Z/14/Z United Kingdom
Wellcome Trust100298/Z/12/Z United Kingdom
Dunn School EPA Studentship United Kingdom
CitationJournal: Cell / Year: 2017
Title: Structural Basis for Mitotic Centrosome Assembly in Flies.
Authors: Feng, Z. / Caballe, A. / Wainman, A. / Johnson, S. / Haensele, A.F.M. / Cottee, M.A. / Conduit, P.T. / Lea, S.M. / Raff, J.W.
History
DepositionFeb 17, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Centrosomin
B: Centrosomin
C: Centrosomin
D: Centrosomin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9256
Polymers32,7944
Non-polymers1312
Water0
1
A: Centrosomin
B: Centrosomin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4623
Polymers16,3972
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1320 Å2
ΔGint-48 kcal/mol
Surface area10860 Å2
MethodPISA
2
C: Centrosomin
D: Centrosomin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4623
Polymers16,3972
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-47 kcal/mol
Surface area10800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.220, 49.220, 211.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein
Centrosomin / CDK5RAP2 / Protein arrow


Mass: 8198.428 Da / Num. of mol.: 4 / Fragment: UNP residues 1082-1148
Source method: isolated from a genetically manipulated source
Details: Fragment: CONSERVED-MOTIF 2 DOMAIN, RESIDUES 1082-1148
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: cnn, Arr, CG4832 / Plasmid: pLip / Details (production host): custom / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P54623
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 2.25 Å3/Da / Density % sol: 45.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 80 mM Sodium cacodylate pH6.5, 160 mM Calcium acetate, 14.4% w/v PEG8K/ 20% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.804→42.626 Å / Num. obs: 7171 / % possible obs: 99.9 % / Redundancy: 10.4 % / CC1/2: 1 / Rmerge(I) obs: 0.069 / Net I/σ(I): 19.7
Reflection shellResolution: 2.804→2.88 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 1.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia20.3.6.3data reduction
AutoSol1.9_1692phasing
RefinementMethod to determine structure: SAD / Resolution: 2.804→42.626 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.38
RfactorNum. reflection% reflectionSelection details
Rfree0.2676 369 5.2 %random selection
Rwork0.2425 ---
obs0.2439 7100 99.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.804→42.626 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1953 0 2 0 1955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031973
X-RAY DIFFRACTIONf_angle_d0.5552626
X-RAY DIFFRACTIONf_dihedral_angle_d12.762802
X-RAY DIFFRACTIONf_chiral_restr0.021298
X-RAY DIFFRACTIONf_plane_restr0.002335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8038-3.20930.39151370.30642235X-RAY DIFFRACTION100
3.2093-4.04290.35641210.27392242X-RAY DIFFRACTION100
4.0429-42.63070.20911110.21762254X-RAY DIFFRACTION100
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)
14.19146.4917-5.74815.6446-6.72575.0088-0.68840.3348-0.8529-0.5587-0.0043-1.21750.6778-0.37010.65241.025-0.01930.23370.95350.26140.908668.5596-8.360111.054
24.16614.1525-4.18437.6316-7.03836.23360.49760.05960.28460.9757-0.09510.1167-1.217-0.5694-0.41530.69970.02640.09710.534-0.03660.62464.71753.003211.2871
31.70263.2852-3.27288.883-6.73356.9932-0.2636-0.464-0.57410.3021-0.6225-1.7694-0.21230.26730.82360.51870.01150.03810.84640.2060.734866.0105-12.567826.434
42.26342.7374-2.62596.7172-5.29674.6260.02120.69530.1037-0.24061.11151.0792-0.0697-1.3288-0.88850.5458-0.007-0.10540.83370.11710.680354.0841-15.18426.7182
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 62 )
2X-RAY DIFFRACTION2chain 'B' and (resid 4 through 62 )
3X-RAY DIFFRACTION3chain 'C' and (resid 4 through 62 )
4X-RAY DIFFRACTION4chain 'D' and (resid 4 through 61 )

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