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- PDB-2fdc: Structural Basis of DNA Damage Recognition and Processing by UvrB... -

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Basic information

Entry
Database: PDB / ID: 2fdc
TitleStructural Basis of DNA Damage Recognition and Processing by UvrB: crystal structure of a UvrB/DNA complex
Components
  • 5'-D(P*CP*GP*GP*CP*TP*CP*CP*AP*TP*CP*TP*CP*TP*AP*CP*CP*GP*CP*AP*A)-3'
  • UvrABC system protein B
KeywordsDNA BINDING PROTEIN/DNA / Protein-DNA complex / UvrB / UvrC / UvrD / UvrA / NER / nucleotide excision repair / DNA 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
Helix Hairpins - #240 / 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 ...Helix Hairpins - #240 / 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 / Helix Hairpins / Helix non-globular / Helicase conserved C-terminal domain / Special / 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
Chem-FLQ / DNA / DNA (> 10) / UvrABC system protein B
Similarity search - Component
Biological speciesBacillus caldotenax (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsTruglio, J.J. / Kisker, C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Structural basis for DNA recognition and processing by UvrB.
Authors: Truglio, J.J. / Karakas, E. / Rhau, B. / Wang, H. / DellaVecchia, M.J. / Van Houten, B. / Kisker, C.
History
DepositionDec 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Remark 600HETEROGEN FLQ IS A FLUORESCEIN ADDUCT. IT IS ONLY PARTIALLY ORDERED IN THE STRUCTURE AND IS LINKED ...HETEROGEN FLQ IS A FLUORESCEIN ADDUCT. IT IS ONLY PARTIALLY ORDERED IN THE STRUCTURE AND IS LINKED TO THE THYMINE 11 THROUGH ATOMS NOT SEEN IN THE DENSITY.
Remark 999SEQUENCE THE AUTHORS STATE THE SEQUENCE DATABASE IS INCORRECT AT THESE RESIDUES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: 5'-D(P*CP*GP*GP*CP*TP*CP*CP*AP*TP*CP*TP*CP*TP*AP*CP*CP*GP*CP*AP*A)-3'
D: 5'-D(P*CP*GP*GP*CP*TP*CP*CP*AP*TP*CP*TP*CP*TP*AP*CP*CP*GP*CP*AP*A)-3'
A: UvrABC system protein B
B: UvrABC system protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,7205
Polymers163,2044
Non-polymers5171
Water00
1
D: 5'-D(P*CP*GP*GP*CP*TP*CP*CP*AP*TP*CP*TP*CP*TP*AP*CP*CP*GP*CP*AP*A)-3'
A: UvrABC system protein B


Theoretical massNumber of molelcules
Total (without water)81,6022
Polymers81,6022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 5'-D(P*CP*GP*GP*CP*TP*CP*CP*AP*TP*CP*TP*CP*TP*AP*CP*CP*GP*CP*AP*A)-3'
B: UvrABC system protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1183
Polymers81,6022
Non-polymers5171
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.265, 153.265, 160.170
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological unit is a monomer. There are two monomers in the asymmetric unit.

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Components

#1: DNA chain 5'-D(P*CP*GP*GP*CP*TP*CP*CP*AP*TP*CP*TP*CP*TP*AP*CP*CP*GP*CP*AP*A)-3'


Mass: 6014.895 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein UvrABC system protein B / UvrB protein / Excinuclease ABC subunit B


Mass: 75587.000 Da / Num. of mol.: 2
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
#3: Chemical ChemComp-FLQ / N-[6-(ACETYLAMINO)HEXYL]-3',6'-DIHYDROXY-3-OXO-3H-SPIRO[2-BENZOFURAN-1,9'-XANTHENE]-6-CARBOXAMIDE / FLUORESCEIN ADDUCT


Mass: 516.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H28N2O7

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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: 3.32 Å3/Da / Density % sol: 62.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20mM MgCl2, 14% PEG3000, 80mM sodium citrate pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 12, 2005
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionRedundancy: 7.8 % / Number: 33350 / Rmerge(I) obs: 0.138 / Χ2: 1.36 / D res high: 3.3 Å / D res low: 50 Å / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.15099.310.0411.1997.4
5.647.110010.0911.2817.8
4.935.6410010.0951.2787.9
4.484.9310010.0971.3237.9
4.164.4810010.131.4647.9
3.914.1610010.1771.347.9
3.723.9110010.2371.4157.9
3.553.7210010.31.5127.9
3.423.5510010.4111.4048
3.33.4210010.5481.3767.9
ReflectionResolution: 3.3→50 Å / Num. all: 33350 / Num. obs: 33350 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Rmerge(I) obs: 0.138 / Χ2: 1.36
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.548 / Num. unique all: 3332 / Χ2: 1.376 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→10 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.873 / SU B: 41.024 / SU ML: 0.32 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.476 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1580 5 %RANDOM
Rwork0.205 ---
all0.207 33350 --
obs0.21 31873 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 71.961 Å2
Baniso -1Baniso -2Baniso -3
1-1.97 Å20.98 Å20 Å2
2--1.97 Å20 Å2
3----2.95 Å2
Refinement stepCycle: LAST / Resolution: 3.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8803 343 32 0 9178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0229372
X-RAY DIFFRACTIONr_bond_other_d0.0030.028552
X-RAY DIFFRACTIONr_angle_refined_deg1.372.02812736
X-RAY DIFFRACTIONr_angle_other_deg0.796319847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.07851085
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.24823.363455
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.42151633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0521597
X-RAY DIFFRACTIONr_chiral_restr0.0820.21429
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210122
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021841
X-RAY DIFFRACTIONr_nbd_refined0.2090.22379
X-RAY DIFFRACTIONr_nbd_other0.180.29792
X-RAY DIFFRACTIONr_nbtor_refined0.1820.24515
X-RAY DIFFRACTIONr_nbtor_other0.0850.25714
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2234
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0690.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.110.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1890.2109
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.22
X-RAY DIFFRACTIONr_mcbond_it1.61325725
X-RAY DIFFRACTIONr_mcbond_other0.22922201
X-RAY DIFFRACTIONr_mcangle_it2.62638812
X-RAY DIFFRACTIONr_scbond_it1.25524402
X-RAY DIFFRACTIONr_scangle_it2.17433924
LS refinement shellResolution: 3.3→3.376 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 105 -
Rwork0.264 2048 -
obs-2153 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6991-0.62130.48491.79230.00011.46560.096-0.3232-0.3662-0.207-0.03480.08070.20290.0986-0.0612-0.10070.1136-0.0346-0.0270.0483-0.09641.50340.6203159.7176
21.525-0.59030.8651.0985-0.48181.71970.197-0.0576-0.2113-0.2122-0.00670.03160.35230.0896-0.1903-0.0430.1195-0.0912-0.0867-0.0147-0.029841.096940.209181.4207
32.2837-2.1939-0.61462.79280.54660.54540.51760.11880.057-0.6623-0.3785-0.1963-0.3252-0.2273-0.1390.2120.19280.0854-0.13090.0007-0.180958.664736.4918133.5855
42.53310.63260.13752.1024-0.27172.3452-0.14740.8519-0.1649-0.2755-0.00010.05660.1778-0.32250.14750.130.0731-0.09980.0977-0.1877-0.234356.827318.601927.9459
51.1912-1.0076-0.40781.7540.29290.47880.11650.01760.0016-0.0988-0.0602-0.0042-0.1543-0.1706-0.05630.0090.1227-0.0098-0.091-0.0084-0.087259.961536.193255.3648
62.2449-1.74031.79182.107-0.22833.20810.3823-0.0015-0.037-0.434-0.369-0.2306-0.0715-0.0797-0.01330.110.07810.0601-0.1725-0.0043-0.091379.931812.7035129.9983
71.1635-1.02211.17692.3395-1.41062.79710.0346-0.0001-0.1312-0.1393-0.0197-0.02260.03570.0799-0.0149-0.01740.04390.0019-0.1514-0.0214-0.034780.57039.809151.4056
84.0804-2.3626-6.03843.022710.554139.04020.84251.190.44562.0648-1.58130.707-0.10380.01450.7388-0.02530.04750.0663-0.09670.0078-0.005664.350121.770471.645
93.1487-2.2884-4.14621.66663.12969.3971-0.0791-0.1947-0.71520.29470.00190.3223-0.020.15990.07720.02170.0070.0397-0.09650.0257-0.0159.611221.018162.7406
1011.8623-11.9243-11.901212.543110.476815.91090.07110.1594-1.4463-0.2223-1.09511.1056-0.28040.0161.0241-0.02530.00280.0266-0.16270.01110.089163.346218.7971137.0519
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AC414 - 593414 - 593
22BD414 - 593414 - 593
33AC5 - 905 - 90
43AC117 - 159117 - 159
53AC320 - 413320 - 413
64BD156 - 247156 - 247
75BD2 - 902 - 90
85BD117 - 155117 - 155
95BD320 - 413320 - 413
106AC243 - 319243 - 319
117BD248 - 319248 - 319
128CA1 - 51 - 5
139CA13 - 1913 - 19
149CE473
1510DB15 - 1915 - 19

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