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- PDB-4c8h: Crystal structure of the C-terminal region of yeast Ctf4, selenom... -

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Basic information

Entry
Database: PDB / ID: 4c8h
TitleCrystal structure of the C-terminal region of yeast Ctf4, selenomethionine protein.
ComponentsCTF4
KeywordsDNA REPLICATION / ADAPTOR PROTEIN / BETA PROPELLER DOMAIN
Function / homology
Function and homology information


establishment of sister chromatid cohesion / Cul8-RING ubiquitin ligase complex / double-strand break repair via break-induced replication / replication fork protection complex / mitotic sister chromatid cohesion / nuclear chromosome / nuclear replication fork / DNA replication initiation / DNA-templated DNA replication / nucleosome assembly ...establishment of sister chromatid cohesion / Cul8-RING ubiquitin ligase complex / double-strand break repair via break-induced replication / replication fork protection complex / mitotic sister chromatid cohesion / nuclear chromosome / nuclear replication fork / DNA replication initiation / DNA-templated DNA replication / nucleosome assembly / mitotic cell cycle / DNA repair / chromatin binding / identical protein binding / nucleus
Similarity search - Function
: / DNA polymerase alpha-binding protein Ctf4, C-terminal domain / Minichromosome loss protein Mcl1, middle region / Minichromosome loss protein, Mcl1, middle region / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
DNA polymerase alpha-binding protein
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.691 Å
AuthorsSimon, A.C. / Pellegrini, L.
CitationJournal: Nature / Year: 2014
Title: A Ctf4 Trimer Couples the Cmg Helicase to DNA Polymerase Alpha in the Eukaryotic Replisome
Authors: Simon, A.C. / Zhou, J.C. / Perera, R.L. / Vandeursen, F. / Evrin, C. / Ivanova, M.E. / Kilkenny, M.L. / Renault, L. / Kjaer, S. / Matak-Vinkovic, D. / Labib, K. / Costa, A. / Pellegrini, L.
History
DepositionOct 1, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2May 21, 2014Group: Database references
Revision 1.3Jun 18, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CTF4
B: CTF4
C: CTF4


Theoretical massNumber of molelcules
Total (without water)165,0313
Polymers165,0313
Non-polymers00
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-37.4 kcal/mol
Surface area53720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.294, 118.428, 155.697
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein CTF4


Mass: 55010.215 Da / Num. of mol.: 3 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PRSFDUET-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: Q01454
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.07 Å3/Da / Density % sol: 59.9 % / Description: NONE
Crystal growDetails: 0.2 M TRI-SODIUM CITRATE PH 6.2, 7-9% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9794
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.69→49.19 Å / Num. obs: 55547 / % possible obs: 99.5 % / Redundancy: 26.7 % / Biso Wilson estimate: 62.93 Å2 / Rmerge(I) obs: 0.23 / Net I/σ(I): 17.4
Reflection shellResolution: 2.69→2.77 Å / Redundancy: 23.9 % / Rmerge(I) obs: 3.38 / Mean I/σ(I) obs: 1.1 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.691→49.188 Å / SU ML: 0.35 / σ(F): 0.35 / Phase error: 25.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2248 5382 5.1 %
Rwork0.1895 --
obs0.1913 55373 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.4 Å2
Refinement stepCycle: LAST / Resolution: 2.691→49.188 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10253 0 0 163 10416
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310513
X-RAY DIFFRACTIONf_angle_d0.64514238
X-RAY DIFFRACTIONf_dihedral_angle_d10.4213896
X-RAY DIFFRACTIONf_chiral_restr0.0271545
X-RAY DIFFRACTIONf_plane_restr0.0031826
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.691-2.72160.41161510.33882729X-RAY DIFFRACTION82
2.7216-2.75360.39271530.33243450X-RAY DIFFRACTION100
2.7536-2.78720.3351820.29843307X-RAY DIFFRACTION100
2.7872-2.82250.3341790.29753412X-RAY DIFFRACTION100
2.8225-2.85960.31681560.27973333X-RAY DIFFRACTION100
2.8596-2.89880.28811680.27853369X-RAY DIFFRACTION100
2.8988-2.94020.30361620.26763341X-RAY DIFFRACTION100
2.9402-2.98410.35661960.27283364X-RAY DIFFRACTION100
2.9841-3.03070.28861640.26483378X-RAY DIFFRACTION100
3.0307-3.08040.30911830.25613338X-RAY DIFFRACTION100
3.0804-3.13350.32741680.23613383X-RAY DIFFRACTION100
3.1335-3.19050.28182030.25113379X-RAY DIFFRACTION100
3.1905-3.25180.26941810.22773358X-RAY DIFFRACTION100
3.2518-3.31820.27731610.21463344X-RAY DIFFRACTION100
3.3182-3.39030.22611910.20443377X-RAY DIFFRACTION100
3.3903-3.46920.25362310.19673338X-RAY DIFFRACTION100
3.4692-3.55590.24221650.20423356X-RAY DIFFRACTION100
3.5559-3.6520.29172050.23307X-RAY DIFFRACTION100
3.652-3.75940.22631910.18663352X-RAY DIFFRACTION100
3.7594-3.88070.25731690.19453384X-RAY DIFFRACTION100
3.8807-4.01940.21741950.17313358X-RAY DIFFRACTION100
4.0194-4.18020.18721670.14683377X-RAY DIFFRACTION100
4.1802-4.37040.13521700.14253378X-RAY DIFFRACTION100
4.3704-4.60060.17781680.14743366X-RAY DIFFRACTION100
4.6006-4.88860.17351570.13913403X-RAY DIFFRACTION100
4.8886-5.26570.18021700.14893344X-RAY DIFFRACTION100
5.2657-5.79480.20061830.17323366X-RAY DIFFRACTION100
5.7948-6.63160.22142330.18243327X-RAY DIFFRACTION100
6.6316-8.34850.19561870.17083356X-RAY DIFFRACTION100
8.3485-49.1960.17171930.1783355X-RAY DIFFRACTION100

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