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- PDB-6o8g: Crystal structure of UvrB bound to fully duplex DNA -

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Basic information

Entry
Database: PDB / ID: 6o8g
TitleCrystal structure of UvrB bound to fully duplex DNA
Components
  • DNA (5'-D(*GP*GP*TP*AP*GP*CP*GP*CP*GP*AP*TP*GP*GP*AP*GP*A)-3')
  • DNA (5'-D(*TP*CP*TP*CP*CP*AP*TP*CP*GP*CP*GP*CP*TP*AP*C)-3')
  • UvrABC system protein B
KeywordsDNA BINDING PROTEIN/DNA / DNA repair / nucleotide excision 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
ADENOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / UvrABC system protein B
Similarity search - Component
Biological speciesBacillus caldotenax (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsLee, S.-J. / Sung, R.-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: UvrABC system protein B
D: DNA (5'-D(*TP*CP*TP*CP*CP*AP*TP*CP*GP*CP*GP*CP*TP*AP*C)-3')
E: DNA (5'-D(*GP*GP*TP*AP*GP*CP*GP*CP*GP*AP*TP*GP*GP*AP*GP*A)-3')
F: DNA (5'-D(*TP*CP*TP*CP*CP*AP*TP*CP*GP*CP*GP*CP*TP*AP*C)-3')
G: DNA (5'-D(*GP*GP*TP*AP*GP*CP*GP*CP*GP*AP*TP*GP*GP*AP*GP*A)-3')
H: DNA (5'-D(*TP*CP*TP*CP*CP*AP*TP*CP*GP*CP*GP*CP*TP*AP*C)-3')
I: DNA (5'-D(*GP*GP*TP*AP*GP*CP*GP*CP*GP*AP*TP*GP*GP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,34014
Polymers233,0009
Non-polymers1,3405
Water46826
1
A: UvrABC system protein B
D: DNA (5'-D(*TP*CP*TP*CP*CP*AP*TP*CP*GP*CP*GP*CP*TP*AP*C)-3')
E: DNA (5'-D(*GP*GP*TP*AP*GP*CP*GP*CP*GP*AP*TP*GP*GP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1175
Polymers77,6673
Non-polymers4502
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-43 kcal/mol
Surface area28610 Å2
MethodPISA
2
B: UvrABC system protein B
F: DNA (5'-D(*TP*CP*TP*CP*CP*AP*TP*CP*GP*CP*GP*CP*TP*AP*C)-3')
G: DNA (5'-D(*GP*GP*TP*AP*GP*CP*GP*CP*GP*AP*TP*GP*GP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1295
Polymers77,6673
Non-polymers4632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-43 kcal/mol
Surface area29320 Å2
MethodPISA
3
C: UvrABC system protein B
H: DNA (5'-D(*TP*CP*TP*CP*CP*AP*TP*CP*GP*CP*GP*CP*TP*AP*C)-3')
I: DNA (5'-D(*GP*GP*TP*AP*GP*CP*GP*CP*GP*AP*TP*GP*GP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0944
Polymers77,6673
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-37 kcal/mol
Surface area28960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)170.685, 201.181, 62.664
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 68157.453 Da / Num. of mol.: 3
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, 6 molecules DFHEGI

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


Mass: 4480.911 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*GP*TP*AP*GP*CP*GP*CP*GP*AP*TP*GP*GP*AP*GP*A)-3')


Mass: 5028.266 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 31 molecules

#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, pH 7.5, 0.02 M magnesium chloride, 20-22% poly(acryl acid sodium salt) 5100

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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: Oct 28, 2011
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: 2.63→50 Å / Num. obs: 64310 / % possible obs: 99.8 % / Redundancy: 6.2 % / Net I/σ(I): 18.9
Reflection shellResolution: 2.63→2.78 Å / Num. unique obs: 9258

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→48.24 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.906 / SU B: 15.926 / SU ML: 0.326 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.373 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2738 3254 5.1 %RANDOM
Rwork0.22 ---
obs0.2228 61005 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 155.98 Å2 / Biso mean: 69.098 Å2 / Biso min: 35.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 2.64→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13662 1874 83 26 15645
Biso mean--89.32 53.15 -
Num. residues----1784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01816073
X-RAY DIFFRACTIONr_bond_other_d0.0010.0214658
X-RAY DIFFRACTIONr_angle_refined_deg0.9951.86422115
X-RAY DIFFRACTIONr_angle_other_deg2.364333681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.61351685
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.82823.156713
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.411152547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.24415162
X-RAY DIFFRACTIONr_chiral_restr0.0590.22398
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216776
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023708
LS refinement shellResolution: 2.635→2.703 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 226 -
Rwork0.35 4458 -
all-4684 -
obs--99.74 %

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