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- PDB-3oq0: Crystal Structure of motif N of Saccharomyces cerevisiae Dbf4 -

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Basic information

Entry
Database: PDB / ID: 3oq0
TitleCrystal Structure of motif N of Saccharomyces cerevisiae Dbf4
ComponentsDBF4
KeywordsCELL CYCLE / DDK / BRCT / Rad53 / replication checkpoint / FHA domain / regulatory subunit of DDK / cdc7 / phosphorylation / nuclear
Function / homology
Function and homology information


positive regulation of DNA replication initiation / positive regulation of kinetochore assembly / positive regulation of meiotic DNA double-strand break formation / negative regulation of exit from mitosis / Dbf4-dependent protein kinase complex / positive regulation of meiosis I / regulation of cell cycle phase transition / positive regulation of nuclear cell cycle DNA replication / premeiotic DNA replication / Activation of the pre-replicative complex ...positive regulation of DNA replication initiation / positive regulation of kinetochore assembly / positive regulation of meiotic DNA double-strand break formation / negative regulation of exit from mitosis / Dbf4-dependent protein kinase complex / positive regulation of meiosis I / regulation of cell cycle phase transition / positive regulation of nuclear cell cycle DNA replication / premeiotic DNA replication / Activation of the pre-replicative complex / Activation of ATR in response to replication stress / mitotic DNA replication checkpoint signaling / DNA replication origin binding / chromosome, centromeric region / DNA replication initiation / protein serine/threonine kinase activator activity / chromosome segregation / positive regulation of protein phosphorylation / cell division / centrosome / chromatin / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Regulatory subunit Dfp1/Him1, central region / Dfp1/Him1, central region / Zinc finger, DBF-type / DBF-type zinc finger superfamily / DBF zinc finger / Zinc finger DBF4-type profile. / Zinc finger in DBF-like proteins / BRCT domain / BRCT domain superfamily / Rossmann fold ...Regulatory subunit Dfp1/Him1, central region / Dfp1/Him1, central region / Zinc finger, DBF-type / DBF-type zinc finger superfamily / DBF zinc finger / Zinc finger DBF4-type profile. / Zinc finger in DBF-like proteins / BRCT domain / BRCT domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DDK kinase regulatory subunit DBF4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsMatthews, L.A. / Jones, D.R. / Prasad, A.A. / Duncker, B.P. / Guarne, A.
Citation
Journal: To be Published
Title: Crystal Structure of Saccharomyces cerevisiae Dbf4-motif N
Authors: Matthews, L.A. / Jones, D.R. / Prasad, A.A. / Duncker, B.P. / Guarne, A.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Crystallization and preliminary X-ray diffraction analysis of motif N from Saccharomyces cerevisiae Dbf4
Authors: Matthews, L.A. / Duong, A. / Prasad, A.A. / Duncker, B.P. / Guarne, A.
History
DepositionSep 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DBF4
B: DBF4
C: DBF4
D: DBF4
E: DBF4
F: DBF4
G: DBF4
H: DBF4
I: DBF4
J: DBF4


Theoretical massNumber of molelcules
Total (without water)177,46510
Polymers177,46510
Non-polymers00
Water1,67593
1
A: DBF4


Theoretical massNumber of molelcules
Total (without water)17,7461
Polymers17,7461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DBF4


Theoretical massNumber of molelcules
Total (without water)17,7461
Polymers17,7461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DBF4


Theoretical massNumber of molelcules
Total (without water)17,7461
Polymers17,7461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DBF4


Theoretical massNumber of molelcules
Total (without water)17,7461
Polymers17,7461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: DBF4


Theoretical massNumber of molelcules
Total (without water)17,7461
Polymers17,7461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: DBF4


Theoretical massNumber of molelcules
Total (without water)17,7461
Polymers17,7461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: DBF4


Theoretical massNumber of molelcules
Total (without water)17,7461
Polymers17,7461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: DBF4


Theoretical massNumber of molelcules
Total (without water)17,7461
Polymers17,7461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: DBF4


Theoretical massNumber of molelcules
Total (without water)17,7461
Polymers17,7461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: DBF4


Theoretical massNumber of molelcules
Total (without water)17,7461
Polymers17,7461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.221, 79.358, 127.419
Angle α, β, γ (deg.)90.00, 110.74, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A resid 120:220
211chain F resid 120:220
112chain B resid 123:215
212chain G resid 123:215
113chain C resid 122:221
213chain H resid 122:221
114chain D resid 122:224
214chain I resid 122:224
115chain E resid 123:217
215chain J resid 123:217

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein
DBF4 / / Protein DNA52


Mass: 17746.475 Da / Num. of mol.: 10 / Fragment: residues 120-250
Source method: isolated from a genetically manipulated source
Details: Dbf4 residues 120-250 cloned in the multicloning site of pET15b using NdeI-BamHI
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: D4205, DBF4, DNA52, YD9609.07C, YDR052C / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)STARpRarepLysS / References: UniProt: P32325
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 29% PEG 400, 0.05 M MgCl2, 0.1 M TRIS pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 2, 2009 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 46363 / Num. obs: 46033 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.1 / Rsym value: 0.07 / Net I/σ(I): 16.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.7-2.757.20.7952.820.571199.1
7.32-506.40.05519.310.056198.6
5.81-7.326.80.07320.640.073199.4
5.08-5.816.90.07120.180.069199.5
4.62-5.086.90.05723.970.055199.5
4.29-4.626.90.06223.190.059199.5
4.03-4.2970.06821.990.062199.6
3.83-4.0370.07720.340.073199.4
3.66-3.8370.08623.970.074199.5
3.52-3.667.10.08824.110.059199.4
3.4-3.527.10.11618.90.1199.5
3.3-3.47.10.14115.420.114199.2
3.2-3.37.10.1712.570.139199.3
3.12-3.27.10.2239.440.185199.3
3.04-3.127.10.2638.170.204199.3
2.97-3.047.10.3416.260.276199.4
2.91-2.977.20.4235.110.333199.2
2.85-2.917.10.5373.960.416199.2
2.8-2.857.20.5893.610.454199.1
2.75-2.87.20.73230.52199.2

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.4_159)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→35.52 Å / SU ML: 0.39 / σ(F): 1 / Phase error: 26.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2441 2233 5.07 %
Rwork0.2046 --
obs0.2066 44042 94.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.796 Å2 / ksol: 0.339 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-21.5409 Å20 Å20.1039 Å2
2--0.9392 Å2-0 Å2
3----22.48 Å2
Refinement stepCycle: LAST / Resolution: 2.7→35.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8240 0 0 93 8333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098398
X-RAY DIFFRACTIONf_angle_d1.16111280
X-RAY DIFFRACTIONf_dihedral_angle_d17.7623188
X-RAY DIFFRACTIONf_chiral_restr0.0741290
X-RAY DIFFRACTIONf_plane_restr0.0031400
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A855X-RAY DIFFRACTIONPOSITIONAL
12F855X-RAY DIFFRACTIONPOSITIONAL0.02
21B780X-RAY DIFFRACTIONPOSITIONAL
22G780X-RAY DIFFRACTIONPOSITIONAL0.016
31C834X-RAY DIFFRACTIONPOSITIONAL
32H834X-RAY DIFFRACTIONPOSITIONAL0.016
41D868X-RAY DIFFRACTIONPOSITIONAL
42I868X-RAY DIFFRACTIONPOSITIONAL0.016
51E801X-RAY DIFFRACTIONPOSITIONAL
52J801X-RAY DIFFRACTIONPOSITIONAL0.018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.75870.33311320.28062307X-RAY DIFFRACTION85
2.7587-2.82290.30131230.27322402X-RAY DIFFRACTION87
2.8229-2.89340.29891110.28012424X-RAY DIFFRACTION88
2.8934-2.97160.34191400.26872421X-RAY DIFFRACTION90
2.9716-3.0590.31351390.26272533X-RAY DIFFRACTION92
3.059-3.15770.31881190.25232604X-RAY DIFFRACTION94
3.1577-3.27050.25671470.23282633X-RAY DIFFRACTION96
3.2705-3.40130.28181540.22062640X-RAY DIFFRACTION97
3.4013-3.5560.26131240.19632728X-RAY DIFFRACTION98
3.556-3.74330.22671430.18842718X-RAY DIFFRACTION98
3.7433-3.97750.20741630.17812688X-RAY DIFFRACTION98
3.9775-4.28410.20561330.17262696X-RAY DIFFRACTION97
4.2841-4.71440.19981400.15572721X-RAY DIFFRACTION99
4.7144-5.39450.18181440.15382715X-RAY DIFFRACTION99
5.3945-6.78870.21821550.18292779X-RAY DIFFRACTION99
6.7887-35.52340.20351660.19042800X-RAY DIFFRACTION99

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