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- PDB-8j09: Crystal structure of protein 3745 -

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Basic information

Entry
Database: PDB / ID: 8j09
TitleCrystal structure of protein 3745
Components
  • Cell division control protein 45
  • DNA replication regulator SLD3
KeywordsREPLICATION / DNA replication / p45 recruitment / S3
Function / homology
Function and homology information


mitotic DNA replication preinitiation complex assembly / chromatin => GO:0000785 / Activation of the pre-replicative complex / CMG complex / Activation of ATR in response to replication stress / DNA replication preinitiation complex / replication fork protection complex / double-strand break repair via break-induced replication / DNA unwinding involved in DNA replication / nuclear replication fork ...mitotic DNA replication preinitiation complex assembly / chromatin => GO:0000785 / Activation of the pre-replicative complex / CMG complex / Activation of ATR in response to replication stress / DNA replication preinitiation complex / replication fork protection complex / double-strand break repair via break-induced replication / DNA unwinding involved in DNA replication / nuclear replication fork / DNA replication origin binding / chromosome, centromeric region / DNA replication initiation / single-stranded DNA binding / cell cycle / chromatin binding / nucleus
Similarity search - Function
Sld3, N-terminal / Sld3 N-terminal domain / DNA replication regulator Sld3, C-terminal / DNA replication regulator Sld3 / DNA replication regulator SLD3, STD domain / CDC45 family / CDC45-like protein
Similarity search - Domain/homology
DNA replication regulator SLD3 / Cell division control protein 45
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsLi, H. / Yao, M.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21H01754 Japan
Japan Agency for Medical Research and Development (AMED)JP18am0101071 Japan
Japan Agency for Medical Research and Development (AMED)JP19am0101083 Japan
CitationJournal: To Be Published
Title: Structural and functional insights into a process of complex formation by 3745
Authors: Li, H. / Yao, M.
History
DepositionApr 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA replication regulator SLD3
B: Cell division control protein 45


Theoretical massNumber of molelcules
Total (without water)105,4432
Polymers105,4432
Non-polymers00
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-19 kcal/mol
Surface area36380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.771, 107.569, 128.283
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein DNA replication regulator SLD3


Mass: 31118.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: SLD3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P53135
#2: Protein Cell division control protein 45


Mass: 74324.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288c / Gene: CDC45 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q08032
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.32 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M sodium acetate, 0.1M Bis-Tris propane (pH6.5: pH8.5 = 3:7), 20%(w/v) PEG33500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.605→50 Å / Num. obs: 30622 / % possible obs: 99.92 % / Redundancy: 6.6 % / Biso Wilson estimate: 43.86 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1268 / Net I/av σ(I): 2.02 / Net I/σ(I): 13.32
Reflection shellResolution: 2.605→2.703 Å / Rmerge(I) obs: 0.9571 / Num. unique obs: 3000 / CC1/2: 0.727

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHENIX1.16_3549model building
PHENIX1.16_3549phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.61→43.47 Å / SU ML: 0.3378 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.4795
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2624 1570 5.13 %
Rwork0.2189 29052 -
obs0.2212 30622 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.07 Å2
Refinement stepCycle: LAST / Resolution: 2.61→43.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6476 0 0 40 6516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00256596
X-RAY DIFFRACTIONf_angle_d0.62688912
X-RAY DIFFRACTIONf_chiral_restr0.04041013
X-RAY DIFFRACTIONf_plane_restr0.00341123
X-RAY DIFFRACTIONf_dihedral_angle_d2.85224000
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.61-2.690.35971400.30252590X-RAY DIFFRACTION99.53
2.69-2.790.38011400.29152585X-RAY DIFFRACTION99.82
2.79-2.90.31791400.27842592X-RAY DIFFRACTION100
2.9-3.030.34151530.27232612X-RAY DIFFRACTION100
3.03-3.190.28561440.26852607X-RAY DIFFRACTION99.96
3.19-3.390.32741530.24872620X-RAY DIFFRACTION100
3.39-3.650.30491400.23352625X-RAY DIFFRACTION100
3.65-4.020.2521320.20052637X-RAY DIFFRACTION100
4.02-4.60.24361440.18042665X-RAY DIFFRACTION100
4.6-5.790.2211340.1892702X-RAY DIFFRACTION99.93
5.79-43.470.17071500.18142817X-RAY DIFFRACTION99.87

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