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- PDB-2nmv: Damage detection by the UvrABC pathway: Crystal structure of UvrB... -

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Basic information

Entry
Database: PDB / ID: 2nmv
TitleDamage detection by the UvrABC pathway: Crystal structure of UvrB bound to fluorescein-adducted DNA
Components
  • (UvrABC system protein ...) x 2
  • 5'-D(P*TP*TP*TP*TP*T)-3'
KeywordsHYDROLASE/DNA / Protein-DNA complex / T-fluorescein / hairpin / HYDROLASE-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
Penicillin-binding protein 1b fold / Penicillin-binding protein 1b domain / 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 ...Penicillin-binding protein 1b fold / Penicillin-binding protein 1b domain / 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 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID / N-METHYLACETAMIDE / DNA / UvrABC system protein B
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsWaters, T.R. / Eryilmaz, J. / Geddes, S. / Barrett, T.E.
CitationJournal: Febs Lett. / Year: 2006
Title: Damage detection by the UvrABC pathway: crystal structure of UvrB bound to fluorescein-adducted DNA
Authors: Waters, T.R. / Eryilmaz, J. / Geddes, S. / Barrett, T.E.
History
DepositionOct 23, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: 5'-D(P*TP*TP*TP*TP*T)-3'
A: UvrABC system protein B
B: UvrABC system protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2556
Polymers82,4223
Non-polymers8333
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.410, 95.597, 97.878
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 1 types, 1 molecules D

#1: DNA chain 5'-D(P*TP*TP*TP*TP*T)-3'


Mass: 1476.007 Da / Num. of mol.: 1 / Source method: obtained synthetically

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UvrABC system protein ... , 2 types, 2 molecules AB

#2: Protein UvrABC system protein B / Protein uvrB / Excinuclease ABC subunit B / Protein dinA


Mass: 76440.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: uvrB / Plasmid: pET8c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 pLysS
References: UniProt: P37954, Hydrolases; Acting on ester bonds
#3: Protein/peptide UvrABC system protein B / Protein uvrB / Excinuclease ABC subunit B / Protein dinA


Mass: 4506.226 Da / Num. of mol.: 1 / Fragment: residues 622-659
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: uvrB / Plasmid: pET8c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 pLysS
References: UniProt: P37954, Hydrolases; Acting on ester bonds

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Non-polymers , 3 types, 3 molecules

#4: Chemical ChemComp-NML / N-METHYLACETAMIDE


Mass: 73.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO
#5: Chemical ChemComp-FLU / 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID / FLUORESCEIN / Fluorescein


Mass: 332.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H12O5
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, 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

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.74 %
Crystal growTemperature: 289 K / pH: 8.5
Details: 18-20% PEG 20000, 0.1M pH 8.5 Tris-Hcl, microbatch, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 2000011
2Tris-HclTris11
3PEG 2000012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 15, 2005 / Details: Bent cylindrical mirror
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.95→68.36 Å / Num. obs: 15109 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 73.7 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 15.9
Reflection shellResolution: 2.95→3.03 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 5.2 / Num. unique all: 1087 / Rsym value: 0.369 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQUANTUMdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2D7D

2d7d


Resolution: 2.95→68.36 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.852 / SU B: 20.806 / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.515 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28074 755 5 %RANDOM
Rwork0.22428 ---
all0.22706 15109 --
obs0.22706 14309 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.348 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20 Å20 Å2
2---2.04 Å20 Å2
3---0.82 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.95→68.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5179 84 48 0 5311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225403
X-RAY DIFFRACTIONr_angle_refined_deg1.7132.0027315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5275654
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00824.038260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.40515938
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8611547
X-RAY DIFFRACTIONr_chiral_restr0.1010.2829
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024055
X-RAY DIFFRACTIONr_nbd_refined0.2460.22515
X-RAY DIFFRACTIONr_nbtor_refined0.3230.23670
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2182
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.24
X-RAY DIFFRACTIONr_mcbond_it0.6961.53356
X-RAY DIFFRACTIONr_mcangle_it1.23425264
X-RAY DIFFRACTIONr_scbond_it1.79932317
X-RAY DIFFRACTIONr_scangle_it3.0524.52051
LS refinement shellResolution: 2.95→3.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 71 -
Rwork0.265 1010 -
obs-1087 99.17 %

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