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- PDB-1d9z: CRYSTAL STRUCTURE OF THE DNA REPAIR PROTEIN UVRB IN COMPLEX WITH ATP -

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Basic information

Entry
Database: PDB / ID: 1d9z
TitleCRYSTAL STRUCTURE OF THE DNA REPAIR PROTEIN UVRB IN COMPLEX WITH ATP
ComponentsEXCINUCLEASE UVRABC COMPONENT UVRB
KeywordsGENE REGULATION / ATP-bound protein / EXCINUCLEASE
Function / homologyUvrB interaction domain / UvrB, YAD/RRR-motif-containing domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / UVR domain profile. / Ultra-violet resistance protein B / Type III restriction enzyme, res subunit / UvrB/uvrC motif / Helicase conserved C-terminal domain / UVR domain superfamily ...UvrB interaction domain / UvrB, YAD/RRR-motif-containing domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / UVR domain profile. / Ultra-violet resistance protein B / Type III restriction enzyme, res subunit / UvrB/uvrC motif / Helicase conserved C-terminal domain / UVR domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Helicase superfamily 1/2, ATP-binding domain / Helicase/UvrB, N-terminal / UvrABC system, subunit B / UVR domain / Helicase, C-terminal / excinuclease ABC activity / excinuclease repair complex / SOS response / nucleotide-excision repair / ATPase activity / DNA binding / ATP binding / cytoplasm / UvrABC system protein B
Function and homology information
Specimen sourceBacillus caldotenax (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 3.15 Å resolution
AuthorsTheis, K. / Chen, P.J. / Skorvaga, M. / Van Houten, B. / Kisker, C.
Citation
Journal: EMBO J. / Year: 1999
Title: Crystal structure of UvrB, a DNA helicase adapted for nucleotide excision repair.
Authors: Theis, K. / Chen, P.J. / Skorvaga, M. / Van Houten, B. / Kisker, C.
#1: Journal: Embo J. / Year: 1999
Title: Strand opening by the UvrA2B complex allows dynamic recognition of DNA damage
Authors: Zou, Y. / Van Houten, B.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 30, 1999 / Release: May 3, 2000
RevisionDateData content typeGroupCategoryProviderType
1.0May 3, 2000Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Oct 4, 2017Structure modelRefinement descriptionsoftware

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EXCINUCLEASE UVRABC COMPONENT UVRB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,0925
Polyers75,4301
Non-polymers6624
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)153.443, 153.443, 80.741
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP 31 2 1

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Components

#1: Protein/peptide EXCINUCLEASE UVRABC COMPONENT UVRB


Mass: 75429.875 Da / Num. of mol.: 1 / Source: (gene. exp.) Bacillus caldotenax (bacteria) / Genus: Bacillus / Plasmid name: PTYB1 / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / References: UniProt: P56981
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Formula: Zn / Zinc
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM

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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

Crystal
IDDensity MatthewsDensity percent sol
13.6466.18
2
Crystal grow
TempCrystal IDMethodpHDetails
2951vapor diffusion9.08 mg/ml UvrB, 500 mM NaCl, 14-18% PEG 6000, 10 mM ZnCl2, 100 mM Bicine pH 9, pH 9.0, VAPOR DIFFUSION, temperature 295K
2952soaking9.05 mM ATP 5 mM MgCl2 500 mM NaCl, 14-18% PEG 6000, 10 mM ZnCl2, 100 mM Bicine pH 9, pH 9.0, Soaking, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
components of the solutions
*PLUS

Crystal ID: 1

IDConcCommon nameSol IDChemical formulaDetails
18 mg/mlproteindrop
2500 mMdropNaCl
320 mMTris-HCldrop
41 mMdithiothreitoldrop
50.1 mMEDTAdrop
60.03 %dodecylmaltosidedrop
714-18 %PEG6000dropor PEG20000
810 mMdropZnCl2
9100 mMBicinedrop
1020 %PEG6000reservoir
11500 mMreservoirNaCl
12100 mMTris-HClreservoir

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Data collection

DiffractionMean temperature: 90 kelvins
SourceSource: SYNCHROTRON / Type: NSLS BEAMLINE X26C / Synchrotron site: NSLS / Beamline: X26C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Collection date: Aug 9, 1999
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 76 Å2 / D resolution high: 3.15 Å / D resolution low: 20 Å / Number all: 19075 / Number obs: 19075 / Observed criterion sigma F: -1000 / Observed criterion sigma I: -3 / Rmerge I obs: 0.14 / NetI over sigmaI: 17.7 / Redundancy: 6 % / Percent possible obs: 100
Reflection shellRmerge I obs: 0.48 / Highest resolution: 3.15 Å / Lowest resolution: 3.32 Å / Number unique all: 2669 / Redundancy: 7 % / Percent possible all: 100
Reflection shell
*PLUS
Percent possible obs: 100 / Rmerge I obs: 0.52 / MeanI over sigI obs: 3.6

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Processing

Software
NameClassification
REFMACrefinement
X-PLORrefinement
MAR345data collection
SCALEPACKdata scaling
RefineDetails: maximum likelyhood / R Free selection details: random / Sigma F: -1000 / Sigma I: -1000 / Stereochemistry target values: Engh & Huber
Least-squares processR factor R free: 0.335 / R factor R work: 0.262 / Highest resolution: 3.15 Å / Lowest resolution: 20 Å / Number reflection R free: 954 / Number reflection all: 19075 / Number reflection obs: 19075 / Percent reflection obs: 100
Refine hist #LASTHighest resolution: 3.15 Å / Lowest resolution: 20 Å
Number of atoms included #LASTProtein: 4632 / Nucleic acid: 0 / Ligand: 34 / Solvent: 0 / Total: 4666
Refine LS restraints
Refine IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d0.031
Software
*PLUS
Name: 'REFMAC AND XPLOR' / Classification: refinement
Least-squares process
*PLUS
R factor obs: 0.262 / Lowest resolution: 2 Å
Refine LS restraints
*PLUS
Refine IDType
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d

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