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- PDB-2d7d: Structural insights into the cryptic DNA dependent ATP-ase activi... -

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Basic information

Entry
Database: PDB / ID: 2d7d
TitleStructural insights into the cryptic DNA dependent ATP-ase activity of UvrB
Components
  • 40-mer from UvrABC system protein B
  • 5'-D(P*TP*TP*T)-3'
  • UvrABC system protein B
KeywordsHYDROLASE/DNA / Helicase / Protein-DNA-ADP ternary complex / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


excinuclease ABC activity / excinuclease repair complex / nucleotide-excision repair, DNA damage recognition / SOS response / ATP hydrolysis activity / DNA binding / ATP binding / cytoplasm
Similarity search - Function
UvrB, YAD/RRR-motif-containing domain / Ultra-violet resistance protein B / Penicillin-binding protein 1b fold / Penicillin-binding protein 1b domain / UvrABC system, subunit B / UVR domain superfamily / UvrB/uvrC motif / UvrB, interaction domain / UvrB interaction domain / UVR domain ...UvrB, YAD/RRR-motif-containing domain / Ultra-violet resistance protein B / Penicillin-binding protein 1b fold / Penicillin-binding protein 1b domain / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DNA / UvrABC system protein B
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBarrett, T.E.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Structural insights into the cryptic DNA-dependent ATPase activity of UvrB
Authors: Eryilmaz, J. / Ceschini, S. / Ryan, J. / Geddes, S. / Waters, T.R. / Barrett, T.E.
#1: Journal: To be Published
Title: Structural insights into the cryptic ATP-ase activity of UvrB
Authors: Eryilmaz, J. / Ceschini, S. / Ryan, J. / Geddes, S. / Waters, T.R. / Barrett, T.E.
History
DepositionNov 18, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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*T)-3'
A: UvrABC system protein B
B: 40-mer from UvrABC system protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4274
Polymers82,0003
Non-polymers4271
Water3,675204
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.231, 98.215, 95.405
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly consists of a full UvrB monomer, a trithymine oligonucleotide, a single molecule of ADP and a helix-loop-helix dimer fragment resulting from proteolysis of UvrB.

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Components

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


Mass: 867.621 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein UvrABC system protein B / UvrB protein / 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: pET 8c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS
References: UniProt: P37954, Hydrolases; Acting on ester bonds
#3: Protein/peptide 40-mer from UvrABC system protein B


Mass: 4692.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: uvrB / Plasmid: pET 8c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS
References: UniProt: P37954, Hydrolases; Acting on ester bonds
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.12 Å3/Da / Density % sol: 41.98 %
Crystal growTemperature: 289 K / Method: microbatch / pH: 8.5
Details: 18-20% (w/v) PEG 10000 0.1M Tris-Hcl, pH 8.5, Microbatch, temperature 289K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 1000011
2Tris-Hcl11
3H2O11
4PEG 1000012
5Tris-Hcl12
6H2O12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 22, 2005 / Details: Mirrors
RadiationMonochromator: Si 111 channel-cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 39593 / Num. obs: 39593 / % possible obs: 96.1 % / Observed criterion σ(F): 2.4 / Observed criterion σ(I): 2.4 / Redundancy: 5.8 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 5.8
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.4 / Num. unique all: 5487 / Rsym value: 0.31 / % possible all: 92.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1D9X

1d9x


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.884 / SU B: 7.237 / SU ML: 0.186 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.292 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28485 1953 4.9 %RANDOM
Rwork0.22679 ---
all0.22961 39593 --
obs0.22961 39593 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.146 Å2
Baniso -1Baniso -2Baniso -3
1-2.03 Å20 Å20 Å2
2---0.85 Å20 Å2
3----1.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.236 Å0.29 Å
Luzzati d res low-30 Å
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5199 61 27 204 5491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225377
X-RAY DIFFRACTIONr_angle_refined_deg1.611.9947283
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.345656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.97624.046262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.41915945
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5621547
X-RAY DIFFRACTIONr_chiral_restr0.1070.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024044
X-RAY DIFFRACTIONr_nbd_refined0.2190.22437
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23656
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2280
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3210.223
X-RAY DIFFRACTIONr_mcbond_it0.781.53384
X-RAY DIFFRACTIONr_mcangle_it1.27325278
X-RAY DIFFRACTIONr_scbond_it2.2132220
X-RAY DIFFRACTIONr_scangle_it3.3964.52005
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 121 -
Rwork0.279 2633 -
obs-2633 91.77 %

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