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- PDB-6oei: Yeast Spc42 N-terminal coiled-coil fused to PDB: 3K2N -

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Basic information

Entry
Database: PDB / ID: 6oei
TitleYeast Spc42 N-terminal coiled-coil fused to PDB: 3K2N
ComponentsSpindle pole body component SPC42,Sigma-54-dependent transcriptional regulator
KeywordsSTRUCTURAL PROTEIN / Yeast Centrosome / Coiled-Coil / Spindle Pole Body
Function / homology
Function and homology information


intermediate layer of spindle pole body / central plaque of spindle pole body / spindle pole body duplication / regulation of microtubule nucleation / structural constituent of cytoskeleton / sequence-specific DNA binding / regulation of DNA-templated transcription / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
Spindle pole body component Spc42 / Spindle pole body component Spc42p / Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type ...Spindle pole body component Spc42 / Spindle pole body component Spc42p / Sigma-54 interaction domain ATP-binding region A signature. / Sigma-54 interaction domain, ATP-binding site 2 / Sigma-54 interaction domain ATP-binding region B signature. / Sigma-54 interaction domain, ATP-binding site 1 / Sigma-54 interaction domain profile. / Sigma-54 interaction domain / RNA polymerase sigma factor 54 interaction domain / DNA binding HTH domain, Fis-type / Bacterial regulatory protein, Fis family / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Homeobox-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Spindle pole body component SPC42 / Sigma-54-dependent transcriptional regulator
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Chlorobaculum tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.58 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 27, 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

Downloads & links

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Assembly

Deposited unit
A: Spindle pole body component SPC42,Sigma-54-dependent transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3843
Polymers34,1481
Non-polymers2362
Water73941
1
A: Spindle pole body component SPC42,Sigma-54-dependent transcriptional regulator
hetero molecules

A: Spindle pole body component SPC42,Sigma-54-dependent transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7696
Polymers68,2962
Non-polymers4734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Buried area7420 Å2
ΔGint-107 kcal/mol
Surface area26850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.664, 193.108, 95.842
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Spindle pole body component SPC42,Sigma-54-dependent transcriptional regulator /


Mass: 34148.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Spc42 Residues 11-130 fused to Sigma-54-dependent transcriptional regulator
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Chlorobaculum tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS) (bacteria)
Strain: ATCC 204508 / S288c, ATCC 49652 / DSM 12025 / NBRC 103806 / TLS
Gene: SPC42, YKL042W, YKL255, CT0108 / Production host: Escherichia coli (E. coli) / References: UniProt: P36094, UniProt: Q8KG60
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 3.36 Å3/Da / Density % sol: 63.44 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Crystals were grown from a 1:1 mixture of 16 mg/ml protein solution containing 20 mM HEPES pH7.6, 100 mM NaCl and well solution containing 100 mM MOPS pH 7.0, 5% (w/v) PEG4K, 5%(w/v) MPD, and 150 mM NaCitrate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.55→100 Å / Num. obs: 14732 / % possible obs: 99.9 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.021 / Rrim(I) all: 0.077 / Χ2: 0.978 / Net I/av σ(I): 34.4 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.55-2.5711.30.5373530.9840.1620.5620.86899.4
2.57-2.5912.10.6033500.9810.1790.630.8599.7
2.59-2.6212.90.6913580.9290.1980.7190.845100
2.62-2.6413.40.6233650.9660.1760.6480.871100
2.64-2.6713.80.623840.9670.1720.6440.874100
2.67-2.69140.6183430.9650.1710.6410.862100
2.69-2.7214.20.513600.9770.140.5290.859100
2.72-2.7514.20.5163580.9650.1410.5350.883100
2.75-2.7814.40.4493750.9840.1220.4660.87100
2.78-2.8114.20.3773580.990.1040.3910.908100
2.81-2.8414.40.3263680.9910.0890.3380.887100
2.84-2.8714.20.3123550.9950.0860.3240.882100
2.87-2.9114.30.2143560.9960.0590.2220.915100
2.91-2.9414.40.2413640.9950.0660.250.942100
2.94-2.9814.20.1913760.9970.0520.1980.965100
2.98-3.0214.30.2053540.9960.0560.2130.948100
3.02-3.0714.20.183690.9950.0490.1870.956100
3.07-3.1114.30.1683490.9970.0470.1740.954100
3.11-3.1614.20.1473760.9960.0410.1520.992100
3.16-3.2114.20.1383680.9980.0380.1430.976100
3.21-3.2714.30.1263600.9950.0350.1311.002100
3.27-3.3314.20.1193650.9980.0330.1230.988100
3.33-3.3914.20.1093750.9980.030.1131.006100
3.39-3.46140.0973610.9940.0270.1011.038100
3.46-3.5414.20.0893730.9980.0250.0931.045100
3.54-3.6214.20.0853590.9980.0230.0881.126100
3.62-3.7114.20.0773700.9980.0210.081.143100
3.71-3.81140.0693700.9980.0190.0721.048100
3.81-3.9214.20.0643630.9990.0180.0671.077100
3.92-4.0513.90.0613760.9990.0170.0641.034100
4.05-4.1913.90.0643590.9990.0180.0661.086100
4.19-4.36140.063830.9980.0170.0631.147100
4.36-4.5613.80.0583720.9990.0160.0611.156100
4.56-4.813.80.0633780.9990.0180.0651.275100
4.8-5.113.70.0663680.9980.0190.0681.323100
5.1-5.4913.50.0623820.9990.0180.0641.138100
5.49-6.0513.20.063840.9980.0170.0630.965100
6.05-6.9213.20.0463870.9990.0130.0480.785100
6.92-8.7212.90.04538910.0130.0470.794100
8.72-10011.60.0454190.9990.0140.0470.73596.3

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.58→36.378 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.82
RfactorNum. reflection% reflection
Rfree0.2438 686 5 %
Rwork0.2082 --
obs0.2101 13732 91.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 133.47 Å2 / Biso mean: 52.9433 Å2 / Biso min: 7.59 Å2
Refinement stepCycle: final / Resolution: 2.58→36.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1942 0 16 41 1999
Biso mean--69.7 44.86 -
Num. residues----243
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.58-2.77870.2626910.26171729182062
2.7787-3.05820.31131420.242689283196
3.0582-3.50040.24421480.220228232971100
3.5004-4.4090.23061490.189428402989100
4.409-36.38180.22551560.19362965312199
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)
10.17430.455-0.14044.9102-0.2229-0.8801-0.03530.0597-0.1081-0.80020.0967-0.05670.14480.0659-0.04630.3833-0.20790.0750.1288-0.01450.300426.2487-31.48169.9256
20.81770.3605-0.52661.85780.36222.3082-0.02250.47010.0914-1.8251-0.04360.215-0.3632-0.1294-0.07770.7030.04820.13440.30060.0210.061725.257519.329352.6871
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 60 through 160 )A60 - 160
2X-RAY DIFFRACTION2chain 'A' and (resid 161 through 302 )A161 - 302

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