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- PDB-1c4o: CRYSTAL STRUCTURE OF THE DNA NUCLEOTIDE EXCISION REPAIR ENZYME UV... -

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Basic information

Entry
Database: PDB / ID: 1c4o
TitleCRYSTAL STRUCTURE OF THE DNA NUCLEOTIDE EXCISION REPAIR ENZYME UVRB FROM THERMUS THERMOPHILUS
ComponentsDNA NUCLEOTIDE EXCISION REPAIR ENZYME UVRB
KeywordsREPLICATION / DNA NUCLEOTIDE EXCISION REPAIR / UVRABC / HELICASE / HYPERTHERMOSTABLE PROTEIN
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 nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
UvrABC system protein B
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.5 Å
AuthorsMachius, M. / Henry, L. / Palnitkar, M. / Deisenhofer, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Crystal structure of the DNA nucleotide excision repair enzyme UvrB from Thermus thermophilus.
Authors: Machius, M. / Henry, L. / Palnitkar, M. / Deisenhofer, J.
History
DepositionSep 14, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _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: DNA NUCLEOTIDE EXCISION REPAIR ENZYME UVRB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1047
Polymers76,1351
Non-polymers9696
Water6,053336
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.740, 134.740, 106.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein DNA NUCLEOTIDE EXCISION REPAIR ENZYME UVRB


Mass: 76134.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: PET17B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q56243
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 3.7 Å3/Da / Density % sol: 66.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 4 MICROLITERS PROTEIN (14 MG/ML IN 50 MM TRIS/CL, 1 MM EDTA, 5 MM DTT, 10% (V/ V) GLYCEROL, PH 7.5) WERE MIXED WITH 4 MICROLITERS RESERVOIR SOLUTION (1.7-1.9 M LITHIUM SULFATE, 0.1 M MES, 0. ...Details: 4 MICROLITERS PROTEIN (14 MG/ML IN 50 MM TRIS/CL, 1 MM EDTA, 5 MM DTT, 10% (V/ V) GLYCEROL, PH 7.5) WERE MIXED WITH 4 MICROLITERS RESERVOIR SOLUTION (1.7-1.9 M LITHIUM SULFATE, 0.1 M MES, 0.5% (W/V) BETA-OCTYLGLUCOSIDE, PH 6.0) AND EQUILIBRATED AGAINST 1 ML OF RESERVOIR SOLUTION AT 293 K., VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
pH: 7.5 / Details: Shibata, A., (1999) Acta Crystallogr.D55, 704.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 mg/mlprotein1drop
210 mMbeta-mercaptoehtanol1drop
31 mMEDTA1drop
410 %(v/v)glycerol1drop
550 mMTris-HCl1drop
61.78 Mlithium sulfate1reservoir
70.5 %(w/v)beta-octylglucoside1reservoir
8100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 138 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979
DetectorType: SBC / Detector: CCD / Date: Jun 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→41.82 Å / Num. obs: 176690 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 7 / Net I/σ(I): 26
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.729 / Mean I/σ(I) obs: 1.3 / Rsym value: 72.9 / % possible all: 93.3
Reflection shell
*PLUS
% possible obs: 93.3 %

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Processing

Software
NameVersionClassification
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNS0.5phasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.5→41.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high rms absF: 3556055.56 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2393 1.5 %RANDOM
Rwork0.252 ---
obs0.252 156707 88.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.88 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso mean: 33.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.38 Å21.98 Å20 Å2
2--3.38 Å20 Å2
3----6.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.5→41.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4057 0 60 336 4453
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.358 346 1.6 %
Rwork0.365 21504 -
obs--74.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMMYTOPPAR:BOG.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4MYTOPPAR:BOG.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.05

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