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- PDB-1kft: Solution Structure of the C-Terminal domain of UvrC from E-coli -

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Basic information

Entry
Database: PDB / ID: 1kft
TitleSolution Structure of the C-Terminal domain of UvrC from E-coli
ComponentsExcinuclease ABC subunit C
KeywordsDNA BINDING PROTEIN / helix-hairpin-helix / HhH domain / DNA-binding domain
Function / homology
Function and homology information


excinuclease ABC activity / excinuclease repair complex / SOS response / nucleotide-excision repair / response to radiation / DNA damage response / DNA binding / cytoplasm
Similarity search - Function
UvrC, RNAse H endonuclease domain / UvrABC system, subunit C / UvrC, RNAse H endonuclease domain superfamily / UvrC RNAse H endonuclease domain / UvrC family, homology region profile. / GIY-YIG type nucleases (URI domain) / GIY-YIG endonuclease / GIY-YIG catalytic domain / GIY-YIG domain profile. / GIY-YIG endonuclease superfamily ...UvrC, RNAse H endonuclease domain / UvrABC system, subunit C / UvrC, RNAse H endonuclease domain superfamily / UvrC RNAse H endonuclease domain / UvrC family, homology region profile. / GIY-YIG type nucleases (URI domain) / GIY-YIG endonuclease / GIY-YIG catalytic domain / GIY-YIG domain profile. / GIY-YIG endonuclease superfamily / UVR domain superfamily / UvrB/uvrC motif / Helix-hairpin-helix motif / UVR domain / UVR domain profile. / RuvA domain 2-like / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
UvrABC system protein C / UvrABC system protein C
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / A simulated annealing protocol in Cartesian space was used. Final refinement was done with explicit water.
AuthorsSingh, S. / Folkers, G.E. / Bonvin, A.M.J.J. / Boelens, R. / Wechselberger, R. / Niztayev, A. / Kaptein, R.
CitationJournal: EMBO J. / Year: 2002
Title: Solution structure and DNA-binding properties of the C-terminal domain of UvrC from E.coli
Authors: Singh, S. / Folkers, G.E. / Bonvin, A.M.J.J. / Boelens, R. / Wechselberger, R. / Niztayev, A. / Kaptein, R.
History
DepositionNov 23, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Excinuclease ABC subunit C


Theoretical massNumber of molelcules
Total (without water)8,5801
Polymers8,5801
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)22 / 200no NOE distance violations > 0.5A and lowest energies after refining the best 50 of the initial 200 in explicit water
RepresentativeModel #5fewest violations,lowest energy

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Components

#1: Protein Excinuclease ABC subunit C / UvrC


Mass: 8579.860 Da / Num. of mol.: 1 / Fragment: HhH domain(C-Terminal Domain)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DE3 / Plasmid: pET13b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)-P-Lys-S / References: UniProt: P07028, UniProt: P0A8G0*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1213D 15N-separated NOESY
2323D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM UvrC-CTD 15N labelled 300mM Nacl, 50mM Phosphate buffer 0.2mM complete protease inhibitor 95% H2O, 5% D2O, pH 6.895% H2O/5% D2O
21mM UvrC-CTD 15N 13C doublly labelled 300mM Nacl, 50mM Phosphate buffer 0.2mM complete protease inhibitor 95% H2O, 5% D2O, pH 6.895% H2O/5% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1300mM Nacl, 50mM phosphate buffer 6.8 atmospheric atm300 K
2300mM Nacl, 50mM phosphate buffer 6.8 atmospheric atm300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX5001
Bruker DRXBrukerDRX6002
Varian INOVAVarianINOVA7503

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeversion 1.8Delaglio, F., Grzesiek, S., Vuister, G., Zhu, G., Pfeifer, J., and Bax, A.processing
NMRView4.1.3Bruce A. Johnsondata analysis
ARIA1S.,Jens Linge, Michael Nilgesstructure solution
CNS1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.DeLano,P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang,J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warren.structure solution
CNS1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.DeLano,P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang,J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warren.refinement
RefinementMethod: A simulated annealing protocol in Cartesian space was used. Final refinement was done with explicit water.
Software ordinal: 1
Details: Calculation was done on the basis of 1326 unambiguous and 60 ambiguous distance restraints with the inclusion of 68 dihedral angle constraints.
NMR representativeSelection criteria: fewest violations,lowest energy
NMR ensembleConformer selection criteria: no NOE distance violations > 0.5A and lowest energies after refining the best 50 of the initial 200 in explicit water
Conformers calculated total number: 200 / Conformers submitted total number: 22

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