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- PDB-6oec: Yeast Spc42 Trimeric Coiled-Coil Amino Acids 181-211 fused to PDB... -

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Basic information

Entry
Database: PDB / ID: 6oec
TitleYeast Spc42 Trimeric Coiled-Coil Amino Acids 181-211 fused to PDB: 3H5I
ComponentsResponse regulator/sensory box protein/GGDEF domain protein,Spindle pole body component SPC42
KeywordsSTRUCTURAL PROTEIN / Yeast Centrosome / Spindle Pole Body / Trimeric Coiled-coil
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 / diguanylate cyclase activity / phosphorelay signal transduction system / structural constituent of cytoskeleton / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Spindle pole body component Spc42 / Spindle pole body component Spc42p / : / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / PAS domain / PAS-associated, C-terminal / PAC domain profile. ...Spindle pole body component Spc42 / Spindle pole body component Spc42p / : / Diguanylate cyclase, GGDEF domain / diguanylate cyclase / GGDEF domain profile. / GGDEF domain / PAS domain / PAS-associated, C-terminal / PAC domain profile. / Nucleotide cyclase / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / CheY-like superfamily / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
Spindle pole body component SPC42 / Stage 0 sporulation protein A homolog
Similarity search - Component
Biological speciesCarboxydothermus hydrogenoformans (bacteria)
Saccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.514 Å
AuthorsDrennan, A.C. / Shivaani, K. / Seeger, M.A. / Andreas, M.P. / Gardner, J.M. / Sether, E.K.R. / Jasperson, 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
Revision 1.3Oct 11, 2023Group: 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

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Assembly

Deposited unit
A: Response regulator/sensory box protein/GGDEF domain protein,Spindle pole body component SPC42
B: Response regulator/sensory box protein/GGDEF domain protein,Spindle pole body component SPC42
C: Response regulator/sensory box protein/GGDEF domain protein,Spindle pole body component SPC42
D: Response regulator/sensory box protein/GGDEF domain protein,Spindle pole body component SPC42
E: Response regulator/sensory box protein/GGDEF domain protein,Spindle pole body component SPC42
F: Response regulator/sensory box protein/GGDEF domain protein,Spindle pole body component SPC42
G: Response regulator/sensory box protein/GGDEF domain protein,Spindle pole body component SPC42
H: Response regulator/sensory box protein/GGDEF domain protein,Spindle pole body component SPC42
I: Response regulator/sensory box protein/GGDEF domain protein,Spindle pole body component SPC42
J: Response regulator/sensory box protein/GGDEF domain protein,Spindle pole body component SPC42
K: Response regulator/sensory box protein/GGDEF domain protein,Spindle pole body component SPC42
L: Response regulator/sensory box protein/GGDEF domain protein,Spindle pole body component SPC42
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,03019
Polymers213,74912
Non-polymers2817
Water82946
1
A: Response regulator/sensory box protein/GGDEF domain protein,Spindle pole body component SPC42
B: Response regulator/sensory box protein/GGDEF domain protein,Spindle pole body component SPC42
C: Response regulator/sensory box protein/GGDEF domain protein,Spindle pole body component SPC42
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5175
Polymers53,4373
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6930 Å2
ΔGint-58 kcal/mol
Surface area22270 Å2
MethodPISA
2
D: Response regulator/sensory box protein/GGDEF domain protein,Spindle pole body component SPC42
E: Response regulator/sensory box protein/GGDEF domain protein,Spindle pole body component SPC42
F: Response regulator/sensory box protein/GGDEF domain protein,Spindle pole body component SPC42
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5175
Polymers53,4373
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-63 kcal/mol
Surface area22010 Å2
MethodPISA
3
G: Response regulator/sensory box protein/GGDEF domain protein,Spindle pole body component SPC42
H: Response regulator/sensory box protein/GGDEF domain protein,Spindle pole body component SPC42
I: Response regulator/sensory box protein/GGDEF domain protein,Spindle pole body component SPC42
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5175
Polymers53,4373
Non-polymers802
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-59 kcal/mol
Surface area22020 Å2
MethodPISA
4
J: Response regulator/sensory box protein/GGDEF domain protein,Spindle pole body component SPC42
K: Response regulator/sensory box protein/GGDEF domain protein,Spindle pole body component SPC42
L: Response regulator/sensory box protein/GGDEF domain protein,Spindle pole body component SPC42
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4774
Polymers53,4373
Non-polymers401
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6520 Å2
ΔGint-44 kcal/mol
Surface area22340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.197, 169.723, 122.028
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Response regulator/sensory box protein/GGDEF domain protein,Spindle pole body component SPC42


Mass: 17812.424 Da / Num. of mol.: 12 / Mutation: T193E, S195E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901) (bacteria), (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC BAA-161 / DSM 6008 / Z-2901, ATCC 204508 / S288c
Gene: CHY_0880, SPC42, YKL042W, YKL255 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3ADQ4, UniProt: P36094
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 3.22 Å3/Da / Density % sol: 61.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Crystals grown from 1:1 mixture of 12 mg/ml protein stored in 20 mM HEPES pH 7.6, 100 mM NaCl and a well solution consiting of 100 mM PIPES pH 6.0, 10% (w/v) MEPEG 5K, 700 mM tetramethylamine chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97962 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Aug 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97962 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 88519 / % possible obs: 94.3 % / Redundancy: 6 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.034 / Rrim(I) all: 0.101 / Χ2: 0.744 / Net I/σ(I): 5.3 / Num. measured all: 527628
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.592.90.26181570.6360.1560.3070.32888.1
2.59-2.693.40.23983340.7740.130.2740.36889.7
2.69-2.823.60.21481180.8630.1110.2430.40287.7
2.82-2.964.50.18988050.9280.0880.210.45194.6
2.96-3.155.10.16489010.9610.0710.180.51995.3
3.15-3.395.60.13588930.9770.0550.1470.62995.3
3.39-3.737.10.11490690.9880.0420.1220.81797.1
3.73-4.278.20.09793050.9930.0330.1030.99298.8
4.27-5.388.90.08492960.9940.0280.0890.95198.3
5.38-509.10.06396410.9980.0210.0670.83798.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3H5I

3h5i


Resolution: 2.514→48.142 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 23.68
RfactorNum. reflection% reflection
Rfree0.2493 4392 4.96 %
Rwork0.1949 --
obs0.1976 88485 93.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 119.28 Å2 / Biso mean: 45.9306 Å2 / Biso min: 10.49 Å2
Refinement stepCycle: final / Resolution: 2.514→48.142 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14344 0 7 46 14397
Biso mean--67.72 31.24 -
Num. residues----1846
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.514-2.5430.32671260.26861955208166
2.543-2.5730.30631330.25792611274489
2.573-2.60430.37181250.26442637276289
2.6043-2.63730.30171450.25632616276190
2.6373-2.6720.33341430.24262660280389
2.672-2.70860.30531500.23892651280190
2.7086-2.74730.3071270.23292644277189
2.7473-2.78830.30771260.2372581270787
2.7883-2.83190.30481400.22772570271087
2.8319-2.87830.26471560.21652781293795
2.8783-2.92790.30151560.21892791294795
2.9279-2.98110.28651660.21672803296995
2.9811-3.03850.29661390.2272836297595
3.0385-3.10050.29471490.23412819296896
3.1005-3.16790.32761420.23092870301296
3.1679-3.24160.25041250.22672856298196
3.2416-3.32260.27481590.21642865302495
3.3226-3.41240.25131320.20852827295995
3.4124-3.51280.25411330.20832799293294
3.5128-3.62620.26451500.20152933308398
3.6262-3.75570.24511560.20132959311599
3.7557-3.9060.27441350.19362984311999
3.906-4.08370.24631820.17552938312099
4.0837-4.29890.22191470.15952985313299
4.2989-4.5680.18891420.14442933307597
4.568-4.92040.19291540.14393002315699
4.9204-5.4150.20951540.16732991314599
5.415-6.19710.23111580.19023027318599
6.1971-7.80230.24961580.19643021317998
7.8023-48.15050.17591840.15183148333298

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