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- PDB-3fpn: Crystal structure of UvrA-UvrB interaction domains -

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Basic information

Entry
Database: PDB / ID: 3fpn
TitleCrystal structure of UvrA-UvrB interaction domains
Components
  • Geobacillus stearothermophilus UvrA interaction domain
  • Geobacillus stearothermophilus UvrB interaction domain
KeywordsDNA BINDING PROTEIN / UvrA / UvrB / nucleotide excision repair / DNA repair
Function / homology
Function and homology information


excinuclease repair complex / nucleotide-excision repair / ATP hydrolysis activity / DNA binding / ATP binding
Similarity search - Function
UvrA, interaction domain / UvrA interaction domain / Penicillin-binding protein 1b fold / Penicillin-binding protein 1b domain / UvrABC system, subunit B / Ribosomal protein L1/L10, rRNA-binding domain / UvrB, interaction domain / UvrB interaction domain / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / P-loop containing nucleoside triphosphate hydrolase ...UvrA, interaction domain / UvrA interaction domain / Penicillin-binding protein 1b fold / Penicillin-binding protein 1b domain / UvrABC system, subunit B / Ribosomal protein L1/L10, rRNA-binding domain / UvrB, interaction domain / UvrB interaction domain / Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Geobacillus stearothermophilus UvrB interaction domain / Geobacillus stearothermophilus UvrA interaction domain
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsPakotiprapha, D. / Verdine, G.L. / Jeruzalmi, D.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: A Structural Model for the Damage-sensing Complex in Bacterial Nucleotide Excision Repair.
Authors: Pakotiprapha, D. / Liu, Y. / Verdine, G.L. / Jeruzalmi, D.
History
DepositionJan 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Geobacillus stearothermophilus UvrA interaction domain
B: Geobacillus stearothermophilus UvrB interaction domain


Theoretical massNumber of molelcules
Total (without water)25,7102
Polymers25,7102
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Geobacillus stearothermophilus UvrA interaction domain


Theoretical massNumber of molelcules
Total (without water)13,3481
Polymers13,3481
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Geobacillus stearothermophilus UvrB interaction domain


Theoretical massNumber of molelcules
Total (without water)12,3631
Polymers12,3631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.491, 84.491, 60.874
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Geobacillus stearothermophilus UvrA interaction domain


Mass: 13347.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: 10 / Gene: uvrA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0VX13*PLUS
#2: Protein Geobacillus stearothermophilus UvrB interaction domain


Mass: 12362.920 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Strain: 10 / Gene: uvrB / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D0VX12*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.11 Å3/Da / Density % sol: 41.78 %
Crystal growTemperature: 295 K / Method: hanging drop vapor diffusion / pH: 5
Details: PEG4000, NaCl, sodium acetate, Tris-HCl, pH 5.0, hanging drop vapor diffusion, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
DetectorDate: Oct 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 20904 / % possible obs: 99.9 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.043 / Χ2: 1.077 / Net I/σ(I): 70.679
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.8314.50.44310120.747100
1.83-1.8614.50.34610160.759100
1.86-1.914.40.27810260.767100
1.9-1.9414.50.21410370.797100
1.94-1.9814.40.1810210.8100
1.98-2.0314.40.15310280.84100
2.03-2.0814.50.11610290.885100
2.08-2.1314.50.110320.897100
2.13-2.214.40.08610210.924100
2.2-2.2714.40.07210450.931100
2.27-2.3514.40.06410260.895100
2.35-2.4414.40.05810410.9100
2.44-2.5514.40.05310290.903100
2.55-2.6914.30.05410441.076100
2.69-2.8614.20.05810541.55100
2.86-3.08140.05910562.122100
3.08-3.3913.80.05610662.401100
3.39-3.8813.70.0410671.659100
3.88-4.8813.40.02410850.95899.9
4.88-5012.70.02311690.74998.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.4.0066refinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R6F(residues 131-153 and 200-245, chain A), PDB ENTRY 1T5L (residues 157-250, chain A)

2r6f

1t5l


Resolution: 1.8→49.39 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 1 / SU B: 6.197 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.248 967 4.7 %RANDOM
Rwork0.23 ---
obs0.231 20522 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.08 Å2 / Biso mean: 35.421 Å2 / Biso min: 14.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2---0.5 Å20 Å2
3---1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 0 0 53 1757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221723
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.9762315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6835210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.65622.67486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.67215335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8151523
X-RAY DIFFRACTIONr_chiral_restr0.0960.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021279
X-RAY DIFFRACTIONr_mcbond_it0.6341.51050
X-RAY DIFFRACTIONr_mcangle_it1.18621703
X-RAY DIFFRACTIONr_scbond_it2.0283673
X-RAY DIFFRACTIONr_scangle_it3.4034.5612
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 68 -
Rwork0.239 1328 -
all-1396 -
obs--92.21 %
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)
16.0567-1.59340.06652.95030.18282.32430.0270.0251-0.1936-0.11050.0176-0.05640.1780.1913-0.0447-0.1505-0.03020.007-0.1629-0.0022-0.14923.24058.405413.4841
24.82550.1915-0.72699.95141.51062.3909-0.2635-0.8454-0.1711.26460.3933-0.83420.30210.7493-0.12980.0860.1253-0.07980.2101-0.06050.052718.77613.726220.2899
35.33770.47330.08283.310.5173.6641-0.04610.11160.0836-0.11590.0210.03580.03070.13970.0251-0.1932-0.0115-0.0039-0.1346-0.0042-0.14563.39912.480713.9906
43.4274-0.15271.85914.55460.27293.3612-0.12550.35620.151-0.34770.11040.1095-0.25420.06520.0152-0.1207-0.0509-0.0004-0.0461-0.0041-0.079918.506328.666417.2026
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 38
2X-RAY DIFFRACTION2A39 - 77
3X-RAY DIFFRACTION3A78 - 119
4X-RAY DIFFRACTION4B13 - 106

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