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- PDB-3oa7: Structure of the C-terminal domain of Cnm67, a core component of ... -

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Basic information

Entry
Database: PDB / ID: 3oa7
TitleStructure of the C-terminal domain of Cnm67, a core component of the spindle pole body of Saccharomyces cerevisiae
ComponentsHead morphogenesis protein, Chaotic nuclear migration protein 67 fusion protein
KeywordsSTRUCTURAL PROTEIN / coiled coils / spindle pole body
Function / homology
Function and homology information


outer plaque of mitotic spindle pole body / spindle pole body organization / outer plaque of spindle pole body / central plaque of spindle pole body / viral scaffold / regulation of microtubule nucleation / spindle pole body / sporulation resulting in formation of a cellular spore / virion assembly / mitotic spindle organization ...outer plaque of mitotic spindle pole body / spindle pole body organization / outer plaque of spindle pole body / central plaque of spindle pole body / viral scaffold / regulation of microtubule nucleation / spindle pole body / sporulation resulting in formation of a cellular spore / virion assembly / mitotic spindle organization / meiotic cell cycle / structural constituent of cytoskeleton / cell division / DNA binding / cytoplasm
Similarity search - Function
Septation initiation Sid4-like / Septation initiation / Bacteriophage phi-29 scaffolding protein Gp7 / Capsid assembly scaffolding protein Gp7 / Phi29 scaffolding protein
Similarity search - Domain/homology
Capsid assembly scaffolding protein / Chaotic nuclear migration protein 67
Similarity search - Component
Biological speciesBacillus phage phi29 (virus)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsKlenchin, V.A. / Frye, J.J. / Rayment, I.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure-function analysis of the C-terminal domain of CNM67, a core component of the Saccharomyces cerevisiae spindle pole body.
Authors: Klenchin, V.A. / Frye, J.J. / Jones, M.H. / Winey, M. / Rayment, I.
History
DepositionAug 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 22, 2016Group: Database references
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Structure summary
Category: audit_author / entity_src_gen / software / Item: _audit_author.name
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Head morphogenesis protein, Chaotic nuclear migration protein 67 fusion protein


Theoretical massNumber of molelcules
Total (without water)24,2821
Polymers24,2821
Non-polymers00
Water32418
1
A: Head morphogenesis protein, Chaotic nuclear migration protein 67 fusion protein

A: Head morphogenesis protein, Chaotic nuclear migration protein 67 fusion protein


Theoretical massNumber of molelcules
Total (without water)48,5632
Polymers48,5632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area12310 Å2
ΔGint-100 kcal/mol
Surface area21310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.760, 198.563, 53.232
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-585-

HOH

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Components

#1: Protein Head morphogenesis protein, Chaotic nuclear migration protein 67 fusion protein / Late protein GP7-Cnm67 fusion protein


Mass: 24281.709 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage phi29 (virus), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: 7, CNM67, YNL225C, N1264 / Production host: Escherichia coli (E. coli) / References: UniProt: P13848, UniProt: P53865
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.23 Å3/Da / Density % sol: 61.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 10% monomethyl PEG 5000, 1.0M tetramethyl ammonium chloride, 100 mM CHES, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 16, 2007
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 14536 / Num. obs: 14536 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Rmerge(I) obs: 0.101 / Net I/σ(I): 16.2
Reflection shellResolution: 2.3→2.38 Å / % possible all: 100

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Processing

Software
NameVersionClassification
SOLVEphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 13.059 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27069 719 5.1 %RANDOM
Rwork0.23765 ---
obs0.23931 13508 99.66 %-
all-13554 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 81.842 Å2
Baniso -1Baniso -2Baniso -3
1-2.43 Å20 Å20 Å2
2---1.39 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1585 0 0 18 1603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221610
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.9772170
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0585191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97824.58885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.57315310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6451513
X-RAY DIFFRACTIONr_chiral_restr0.1140.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211207
X-RAY DIFFRACTIONr_mcbond_it5.2836965
X-RAY DIFFRACTIONr_mcangle_it8.62601565
X-RAY DIFFRACTIONr_scbond_it9.1948645
X-RAY DIFFRACTIONr_scangle_it14.29280605
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 51 -
Rwork0.272 955 -
obs--99.31 %
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)
12.96740.17140.764513.2604-3.94454.6061-0.19-0.610.23720.39030.19180.3283-0.0583-0.1271-0.00180.14740.04930.05410.2837-0.0220.211227.09472.83416.602
21.7156-0.0161-1.251.52260.77652.77880.2716-0.0396-0.00230.0051-0.04310.0244-0.06080.0449-0.22860.05550.0082-0.02120.23610.00990.051530.394145.28815.365
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 50
2X-RAY DIFFRACTION1A429 - 432
3X-RAY DIFFRACTION2A433 - 573

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