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- PDB-3uwx: Crystal structure of UvrA-UvrB complex -

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Basic information

Entry
Database: PDB / ID: 3uwx
TitleCrystal structure of UvrA-UvrB complex
Components
  • Excinuclease ABC, A subunit
  • UvrABC system protein B
KeywordsDNA BINDING PROTEIN / UvrA / UvrB / nucleotide excision repair / DNA repair / ABC ATPase / ATP binding / DNA binding
Function / homology
Function and homology information


excinuclease ABC activity / excinuclease repair complex / SOS response / nucleotide-excision repair / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
UvrA, interaction domain / UvrA interaction domain / UvrABC system subunit A / UvrA DNA-binding domain / UvrA DNA-binding domain / UvrB, YAD/RRR-motif-containing domain / Ultra-violet resistance protein B / UvrABC system, subunit B / UVR domain superfamily / UvrB/uvrC motif ...UvrA, interaction domain / UvrA interaction domain / UvrABC system subunit A / UvrA DNA-binding domain / UvrA DNA-binding 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 / ATP-grasp fold, subdomain 1 / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / 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 / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
UvrABC system protein A / UvrABC system protein B / UvrABC system protein A / UvrABC system protein B
Similarity search - Component
Biological speciesGeobacillus (bacteria)
Geobacillus sp. Y412MC52 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.398 Å
AuthorsPakotiprapha, D. / Jeruzalmi, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structure and mechanism of the UvrA-UvrB DNA damage sensor.
Authors: Pakotiprapha, D. / Samuels, M. / Shen, K. / Hu, J.H. / Jeruzalmi, D.
History
DepositionDec 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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
A: Excinuclease ABC, A subunit
B: UvrABC system protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,4565
Polymers186,2592
Non-polymers1963
Water00
1
A: Excinuclease ABC, A subunit
B: UvrABC system protein B
hetero molecules

A: Excinuclease ABC, A subunit
B: UvrABC system protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)372,91110
Polymers372,5194
Non-polymers3926
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Unit cell
Length a, b, c (Å)216.823, 216.823, 116.802
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Excinuclease ABC, A subunit


Mass: 107987.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus (bacteria) / Strain: Y412MC52 / Gene: GYMC52_3203, uvrA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: E8SW61, UniProt: A0A0E0TG05*PLUS
#2: Protein UvrABC system protein B


Mass: 78272.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus sp. Y412MC52 (bacteria) / Strain: Y412MC52 / Gene: GYMC52_3204, uvrB / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS / References: UniProt: E8SW62, UniProt: A0A0E0TGM2*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
Sequence detailsTHE SEQUENCE CORRESPONDS TO BACILLUS (GEOBACILLUS) STEAROTHERMOPHILUS STRAIN 10

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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: 3.69 Å3/Da / Density % sol: 66.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Na/K phosphate, PEG 1000, NaCl, trehalose, pH 8.5, vapor diffusion, sitting drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 4.398→50 Å / Num. obs: 17635 / % possible obs: 96.6 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.101 / Χ2: 1.088 / Net I/σ(I): 6.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
4.4-4.566.70.96214720.987182.7
4.56-4.747.20.816301.033191.1
4.74-4.968.30.77317301.023196.8
4.96-5.229.10.7217751.026199.3
5.22-5.549.40.57118001.091199.7
5.54-5.979.60.47717981.063199.7
5.97-6.579.60.27418161.135199.6
6.57-7.529.40.14218241.178199.7
7.52-9.469.10.06518521.085199.4
9.46-508.60.03719381.18197.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.398→38.065 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.6602 / SU ML: 1.74 / σ(F): 1.34 / Phase error: 38.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3486 899 5.11 %
Rwork0.2876 --
obs0.2906 17600 96.69 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 300 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso max: 884.97 Å2 / Biso mean: 347.3082 Å2 / Biso min: 186.44 Å2
Baniso -1Baniso -2Baniso -3
1--60.8938 Å20 Å2-0 Å2
2---60.8938 Å20 Å2
3---121.7875 Å2
Refinement stepCycle: LAST / Resolution: 4.398→38.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12190 0 3 0 12193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00512409
X-RAY DIFFRACTIONf_angle_d0.79316767
X-RAY DIFFRACTIONf_chiral_restr0.0521888
X-RAY DIFFRACTIONf_plane_restr0.0032197
X-RAY DIFFRACTIONf_dihedral_angle_d15.4244762
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.3984-4.67350.47241320.4452404253685
4.6735-5.03360.38321710.37022725289697
5.0336-5.53880.34021490.29352811296099
5.5388-6.33710.39851570.303628392996100
6.3371-7.9720.35241370.269229093046100
7.972-38.06630.31641530.25843013316699
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)
15.99631.1457-1.70085.20310.36512.43370.52070.0746-0.6875-0.5301-0.0676-1.6704-1.11860.021703.11010.2531-0.35892.98960.54653.668755.0731-19.37934.6749
25.3506-2.4044-0.30661.65950.68032.2770.3619-0.6129-0.58790.1895-0.81070.09570.2998-1.437104.0018-0.375-0.46573.5132-0.10123.054353.65045.103221.109
32.6717-1.82150.31552.1771-1.01844.27091.12070.20610.16990.405-0.87641.0554-0.0696-1.5432-03.6509-0.2684-0.20823.41450.05783.614227.7703-18.938721.9493
41.41432.31982.41281.64961.19740.69720.39010.4722-1.2475-0.119-0.354-0.96220.80210.020203.8789-0.0764-0.22883.45720.39763.392448.51412.6657-13.1575
51.0002-4.9031-4.80570.5345-0.92084.61963.0742.64157.90391.3918-0.7040.4595-2.8141-0.80752.67313.37-0.53330.23744.2854-1.1301-0.0036-7.6916-27.362840.4313
60.29441.0137-0.53360.5583-0.9281.8470.9743-1.06130.0085-4.4847-2.04273.0772-0.3987-0.1145-0.20644.345-0.0022-0.4254.1166-0.16424.667317.330719.812413.5254
75.4386-1.4050.65742.5140.00938.1448-0.84340.6617-1.0478-0.02410.4359-1.1793-0.4487-0.162603.393-0.14290.45442.77990.26963.5625-55.0649-58.387735.5387
80.726-0.3971.04450.2134-0.38621.3088-0.5932-1.1204-1.2791.2513-0.334-2.0597-0.3434-0.1023-03.7829-0.33980.51113.29680.07384.3948-27.5028-71.625520.8745
90.1003-0.16270.01030.36890.0620.03512.94990.3371-3.7523-3.0027-0.40853.59711.3942-7.78880.33523.1928-0.2096-0.20294.67431.47783.8211-36.5825-59.727712.5909
102.2607-2.97362.59141.9493-2.742.2509-0.59950.5537-0.92710.91250.1061.4996-0.6477-0.925203.7531-0.57940.60123.3487-0.63012.8253-25.6878-46.211440.4405
111.8932.4929-2.48723.53240.6723-1.9568-0.0731-0.02030.0927-0.91730.29160.7982-0.7581-1.20810.00024.12390.03350.04913.30850.05793.7054-73.3215-51.923313.8756
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resseq 1:87 or resseq 503:608)A1 - 87
2X-RAY DIFFRACTION1chain A and (resseq 1:87 or resseq 503:608)A503 - 608
3X-RAY DIFFRACTION2chain A and (resseq 609:686 or resseq 843:949)A609 - 686
4X-RAY DIFFRACTION2chain A and (resseq 609:686 or resseq 843:949)A843 - 949
5X-RAY DIFFRACTION3chain A and (resseq 88:117 or resseq 257:273 or resseq 412:502)A88 - 117
6X-RAY DIFFRACTION3chain A and (resseq 88:117 or resseq 257:273 or resseq 412:502)A257 - 273
7X-RAY DIFFRACTION3chain A and (resseq 88:117 or resseq 257:273 or resseq 412:502)A412 - 502
8X-RAY DIFFRACTION4chain A and resseq 687:842A687 - 842
9X-RAY DIFFRACTION5chain A and resseq 118:256A118 - 256
10X-RAY DIFFRACTION6chain A and resseq 274:411A274 - 411
11X-RAY DIFFRACTION7chain B and (resseq 1:89 or resseq 116:150 or resseq 324:346 or resseq 379:411)B1 - 89
12X-RAY DIFFRACTION7chain B and (resseq 1:89 or resseq 116:150 or resseq 324:346 or resseq 379:411)B116 - 150
13X-RAY DIFFRACTION7chain B and (resseq 1:89 or resseq 116:150 or resseq 324:346 or resseq 379:411)B324 - 346
14X-RAY DIFFRACTION7chain B and (resseq 1:89 or resseq 116:150 or resseq 324:346 or resseq 379:411)B379 - 411
15X-RAY DIFFRACTION8chain B and (resseq 252:323 or resseq 347:378)B252 - 323
16X-RAY DIFFRACTION8chain B and (resseq 252:323 or resseq 347:378)B347 - 378
17X-RAY DIFFRACTION9chain B and resseq 90:115B90 - 115
18X-RAY DIFFRACTION10chain B and resseq 151:251B151 - 251
19X-RAY DIFFRACTION11chain B and resseq 412:595B412 - 595

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