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- PDB-6od2: Yeast Spc42 C-terminal Antiparallel Coiled-Coil -

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Basic information

Entry
Database: PDB / ID: 6od2
TitleYeast Spc42 C-terminal Antiparallel Coiled-Coil
ComponentsSpindle pole body component SPC42
KeywordsSTRUCTURAL PROTEIN / Coiled-Coil / Spindle Pole Body
Function / homologySpindle pole body component Spc42 / Spindle pole body component Spc42p / spindle pole body / nucleus / cytoplasm / Spindle pole body component SPC42
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.435 Å
AuthorsDrennan, A.C. / Krishna, S. / Seeger, M.A. / Andreas, M.P. / Gardner, J.M. / Sether, E.K.R. / Jaspersen, S.L. / Rayment, I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01GM105537 United States
CitationJournal: Mol.Biol.Cell / Year: 2019
Title: Structure and function of Spc42 coiled-coils in yeast centrosome assembly and duplication.
Authors: Drennan, A.C. / Krishna, S. / Seeger, M.A. / Andreas, M.P. / Gardner, J.M. / Sether, E.K.R. / Jaspersen, S.L. / Rayment, I.
History
DepositionMar 25, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spindle pole body component SPC42


Theoretical massNumber of molelcules
Total (without water)6,5761
Polymers6,5761
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.499, 36.499, 206.004
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Spindle pole body component SPC42


Mass: 6575.931 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain FostersB) (yeast)
Strain: FostersB / Gene: SPC42, FOSTERSB_2873 / Production host: Escherichia coli (E. coli) / References: UniProt: E7Q664
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.01 Å3/Da / Density % sol: 59.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Crystals were grown from a 1:1 mixture of 12 mg/ml protein stored in 20 mM HEPES pH 7.6, 100 mM NaCl, 0.5 mM TCEP and a well solution containing 80 mM MES pH 6.0, 60% (w/v) MPD, 200 mM NaCl.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Apr 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 3577 / % possible obs: 99.4 % / Redundancy: 18.7 % / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.028 / Rrim(I) all: 0.124 / Χ2: 0.98 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.448.70.4941500.9380.1560.5210.83397.4
2.44-2.499.70.4691660.9540.1450.4920.86699.4
2.49-2.5312.70.4621690.9860.1310.4810.842100
2.53-2.5913.90.5071800.9760.1360.5250.864100
2.59-2.64160.4451620.9920.1140.460.87199.4
2.64-2.718.10.3591700.9930.0850.3690.842100
2.7-2.7719.50.3891730.9790.0920.40.863100
2.77-2.8519.10.3051610.9920.0720.3140.86298.8
2.85-2.9318.70.2751640.9930.0670.2830.95398.8
2.93-3.0222.20.2381910.9910.0540.2441.008100
3.02-3.1321.90.2291680.9960.0520.2351.051100
3.13-3.2623.90.2331800.9950.0490.2381.141100
3.26-3.41220.1911690.9960.0420.1961.134100
3.41-3.5821.80.1681890.9960.0360.1721.211100
3.58-3.8119.50.1441750.990.0350.1491.213100
3.81-4.122.60.1321800.9960.0290.1351.146100
4.1-4.5221.70.1172050.9960.0270.121.042100
4.52-5.17220.1031840.9980.0250.1070.92199.5
5.17-6.5119.50.1021960.9970.0240.1050.83198.5
6.51-5017.20.0792450.9980.0190.0820.71597.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
CRANK2phasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.435→31.609 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 17.97
RfactorNum. reflection% reflection
Rfree0.2641 156 5.02 %
Rwork0.2148 --
obs0.2174 3105 87.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 117.23 Å2 / Biso mean: 41.4613 Å2 / Biso min: 7.1 Å2
Refinement stepCycle: final / Resolution: 2.435→31.609 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms442 0 0 10 452
Biso mean---39.34 -
Num. residues----53
LS refinement shellResolution: 2.4353→31.6117 Å / Rfactor Rfree error: 0 / Total num. of bins used: 1
RfactorNum. reflection% reflection
Rfree0.2641 156 -
Rwork0.2148 2949 -
all-3105 -
obs--88 %

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