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- PDB-3c65: Crystal Structure of Bacillus stearothermophilus UvrC 5' endonucl... -

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Basic information

Entry
Database: PDB / ID: 3c65
TitleCrystal Structure of Bacillus stearothermophilus UvrC 5' endonuclease domain
ComponentsUvrABC system protein C
KeywordsHYDROLASE / UvrC / endonuclease / nucleotide excision repair / DNA repair / RNase H / Cytoplasm / DNA damage / DNA excision / Excision nuclease / SOS response
Function / homology
Function and homology information


excinuclease ABC activity / excinuclease repair complex / SOS response / nucleotide-excision repair / DNA binding / cytoplasm
Similarity search - Function
UvrC, RNAse H endonuclease domain / : / UvrC, RNAse H endonuclease domain / UvrABC system, subunit C / UvrC, RNAse H endonuclease domain superfamily / UvrC RNAse H endonuclease domain / UvrC family, homology region profile. / GIY-YIG type nucleases (URI domain) / GIY-YIG endonuclease / GIY-YIG catalytic domain ...UvrC, RNAse H endonuclease domain / : / UvrC, RNAse H endonuclease domain / UvrABC system, subunit C / UvrC, RNAse H endonuclease domain superfamily / UvrC RNAse H endonuclease domain / UvrC family, homology region profile. / GIY-YIG type nucleases (URI domain) / GIY-YIG endonuclease / GIY-YIG catalytic domain / GIY-YIG domain profile. / GIY-YIG endonuclease superfamily / UVR domain superfamily / UvrB/uvrC motif / UVR domain / UVR domain profile. / RuvA domain 2-like / Helix-hairpin-helix domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
UvrABC system protein C
Similarity search - Component
Biological speciesBacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsPakotiprapha, D. / Bowman, B.R. / Mueller, A.A. / Inuzuka, Y. / Verdine, G.L.
CitationJournal: To be Published
Title: Crystal Structure of Bacillus stearothermophilus UvrC 5' endonuclease domain
Authors: Pakotiprapha, D. / Bowman, B.R. / Mueller, A.A. / Inuzuka, Y. / Verdine, G.L.
History
DepositionFeb 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UvrABC system protein C


Theoretical massNumber of molelcules
Total (without water)25,8671
Polymers25,8671
Non-polymers00
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.779, 81.779, 58.583
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein UvrABC system protein C / Protein uvrC / Excinuclease ABC subunit C


Mass: 25867.391 Da / Num. of mol.: 1 / Fragment: 5' endonuclease domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus stearothermophilus (bacteria) / Strain: 10 / Gene: uvrC / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5KWH6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST FOUR RESIDUES ARE EXPRESSION TAGS

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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: 2.19 Å3/Da / Density % sol: 43.74 %
Crystal growTemperature: 292 K / Method: hanging drop vapor diffusion / pH: 8
Details: Tris-HCl, sodium citrate, sodium acetate, sodium formate, sodium chloride, pH 8.0, hanging drop vapor diffusion, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97927, 0.97941
DetectorDate: Aug 16, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979271
20.979411
ReflectionRedundancy: 11.2 % / Av σ(I) over netI: 9.9 / Number: 197950 / Rmerge(I) obs: 0.076 / Χ2: 1.36 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 17709 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.095099.410.0523.4211.1
3.254.0910010.051.88810.8
2.843.2599.910.071.55811.1
2.582.8499.910.0861.33911.2
2.392.5899.810.0981.07911.2
2.252.3999.810.1050.93611.3
2.142.2599.710.1280.87611.2
2.052.1499.810.1530.83211.2
1.972.0599.610.1910.79911.3
1.91.9799.610.2510.79811.2
ReflectionResolution: 1.9→50 Å / Num. obs: 17709 / % possible obs: 99.8 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.076 / Χ2: 1.357 / Net I/σ(I): 9.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.251 / Num. unique all: 1733 / Χ2: 0.798 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLOMONphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
SHARPphasing
RefinementResolution: 1.9→50 Å / FOM work R set: 0.87 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.221 1533 8.7 %
Rwork0.204 --
obs-15152 85.7 %
Solvent computationBsol: 54.511 Å2
Displacement parametersBiso mean: 21.071 Å2
Baniso -1Baniso -2Baniso -3
1-1.537 Å20 Å20 Å2
2--1.537 Å20 Å2
3----3.073 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1198 0 0 77 1275
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.259
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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