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- PDB-6o8f: Crystal structure of UvrB bound to duplex DNA -

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Basic information

Entry
Database: PDB / ID: 6o8f
TitleCrystal structure of UvrB bound to duplex DNA
Components
  • DNA (5'-D(*GP*CP*CP*GP*TP*AP*TP*GP*CP*CP*AP*AP*TP*CP*TP*AP*GP*AP*GP*C)-3')
  • DNA (5'-D(*GP*CP*TP*CP*TP*AP*GP*AP*TP*TP*TP*TP*CP*AP*TP*AP*CP*GP*GP*C)-3')
  • UvrABC system protein B
KeywordsDNA BINDING PROTEIN/DNA / Nucleotide excision repair / DNA repair / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


excinuclease ABC activity / excinuclease repair complex / SOS response / nucleotide-excision repair / ATP hydrolysis activity / DNA binding / ATP binding / cytoplasm
Similarity search - Function
UvrB, YAD/RRR-motif-containing domain / Ultra-violet resistance protein B / UvrABC system, subunit B / UVR domain superfamily / UvrB/uvrC motif / UvrB, interaction domain / UvrB interaction domain / UVR domain / UVR domain profile. / Helicase/UvrB, N-terminal ...UvrB, YAD/RRR-motif-containing domain / Ultra-violet resistance protein B / UvrABC system, subunit B / UVR domain superfamily / UvrB/uvrC motif / UvrB, interaction domain / UvrB interaction domain / UVR domain / UVR domain profile. / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ACETATE ION / DNA / DNA (> 10) / UvrABC system protein B
Similarity search - Component
Biological speciesBacillus caldotenax (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsLee, S.-J. / Verdine, G.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Res / Year: 2019
Title: Mechanism of DNA Lesion Homing and Recognition by the Uvr Nucleotide Excision Repair System.
Authors: Lee, S.J. / Sung, R.J. / Verdine, G.L.
History
DepositionMar 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UvrABC system protein B
B: UvrABC system protein B
C: DNA (5'-D(*GP*CP*TP*CP*TP*AP*GP*AP*TP*TP*TP*TP*CP*AP*TP*AP*CP*GP*GP*C)-3')
D: DNA (5'-D(*GP*CP*CP*GP*TP*AP*TP*GP*CP*CP*AP*AP*TP*CP*TP*AP*GP*AP*GP*C)-3')
E: DNA (5'-D(*GP*CP*TP*CP*TP*AP*GP*AP*TP*TP*TP*TP*CP*AP*TP*AP*CP*GP*GP*C)-3')
F: DNA (5'-D(*GP*CP*CP*GP*TP*AP*TP*GP*CP*CP*AP*AP*TP*CP*TP*AP*GP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,91612
Polymers160,7256
Non-polymers1926
Water57632
1
A: UvrABC system protein B
C: DNA (5'-D(*GP*CP*TP*CP*TP*AP*GP*AP*TP*TP*TP*TP*CP*AP*TP*AP*CP*GP*GP*C)-3')
D: DNA (5'-D(*GP*CP*CP*GP*TP*AP*TP*GP*CP*CP*AP*AP*TP*CP*TP*AP*GP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5308
Polymers80,3623
Non-polymers1675
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-63 kcal/mol
Surface area31210 Å2
MethodPISA
2
B: UvrABC system protein B
E: DNA (5'-D(*GP*CP*TP*CP*TP*AP*GP*AP*TP*TP*TP*TP*CP*AP*TP*AP*CP*GP*GP*C)-3')
F: DNA (5'-D(*GP*CP*CP*GP*TP*AP*TP*GP*CP*CP*AP*AP*TP*CP*TP*AP*GP*AP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3874
Polymers80,3623
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-45 kcal/mol
Surface area31410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.157, 265.250, 68.315
Angle α, β, γ (deg.)90.000, 114.390, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein UvrABC system protein B / Protein UvrB / Excinuclease ABC subunit B


Mass: 68143.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus caldotenax (bacteria) / Gene: uvrB / Production host: Escherichia coli (E. coli) / References: UniProt: P56981

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DNA chain , 2 types, 4 molecules CEDF

#2: DNA chain DNA (5'-D(*GP*CP*TP*CP*TP*AP*GP*AP*TP*TP*TP*TP*CP*AP*TP*AP*CP*GP*GP*C)-3')


Mass: 6099.952 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*CP*GP*TP*AP*TP*GP*CP*CP*AP*AP*TP*CP*TP*AP*GP*AP*GP*C)-3')


Mass: 6118.968 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 38 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.99 Å3/Da / Density % sol: 58.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM Bis-Tris, pH 6.5, 100 mM ammonium acetate, 17-19% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 13, 2013
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.81→132.62 Å / Num. obs: 45596 / % possible obs: 99.8 % / Redundancy: 3.8 % / Net I/σ(I): 9.1
Reflection shellResolution: 2.81→2.91 Å / Num. unique obs: 4507

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
REFMACrefinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→132.62 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.861 / SU B: 18.389 / SU ML: 0.337 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.385
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2641 2298 5 %RANDOM
Rwork0.2195 ---
obs0.2217 43235 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 122.76 Å2 / Biso mean: 47.397 Å2 / Biso min: 11.59 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.02 Å2
2--0.06 Å20 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 2.81→132.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9556 1620 9 32 11217
Biso mean--51.15 24.47 -
Num. residues----1262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01811533
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210398
X-RAY DIFFRACTIONr_angle_refined_deg1.1781.83615920
X-RAY DIFFRACTIONr_angle_other_deg0.988323924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2851179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4723.246499
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.6151781
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.48715111
X-RAY DIFFRACTIONr_chiral_restr0.0690.21713
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111883
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022620
LS refinement shellResolution: 2.81→2.883 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 174 -
Rwork0.358 3210 -
all-3384 -
obs--99.68 %

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