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- PDB-1e52: Solution structure of Escherichia coli UvrB C-terminal domain -

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Basic information

Entry
Database: PDB / ID: 1.0E+52
TitleSolution structure of Escherichia coli UvrB C-terminal domain
ComponentsEXCINUCLEASE ABC SUBUNIT
KeywordsDNA EXCISION REPAIR / UVRB / DNA REPAIR / UVRC BINDING DOMAIN
Function / homology
Function and homology information


: / excinuclease ABC activity / excinuclease repair complex / nucleotide-excision repair, DNA damage recognition / nucleotide-excision repair, preincision complex assembly / SOS response / nucleotide-excision repair / response to radiation / ATP hydrolysis activity / DNA binding ...: / excinuclease ABC activity / excinuclease repair complex / nucleotide-excision repair, DNA damage recognition / nucleotide-excision repair, preincision complex assembly / SOS response / nucleotide-excision repair / response to radiation / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
UVR domain / UvrB, YAD/RRR-motif-containing domain / Ultra-violet resistance protein B / UvrABC system, subunit B / DNA Excision Repair, Uvrb; Chain A / UVR domain superfamily / UvrB/uvrC motif / UvrB, interaction domain / UvrB interaction domain / UVR domain ...UVR domain / UvrB, YAD/RRR-motif-containing domain / Ultra-violet resistance protein B / UvrABC system, subunit B / DNA Excision Repair, Uvrb; Chain A / 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 / Few Secondary Structures / Irregular / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
UvrABC system protein B / UvrABC system protein B
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsAlexandrovich, A.A. / Kelly, G.G. / Frenkiel, T.A. / Moolenaar, G.F. / Goosen, N.N. / Sanderson, M.R. / Lane, A.N.
CitationJournal: J.Biomol.Struct.Dyn. / Year: 2001
Title: Solution Structure, Hydrodynamics and Thermodynamics of the Uvrb C-Terminal Domain.
Authors: Alexandrovich, A.A. / Czisch, M.M. / Frenkiel, T.T. / Kelly, G.G. / Goosen, N.N. / Moolenaar, G.G. / Chowdhry, B.B. / Sanderson, M.M. / Lane, A.A.
History
DepositionJul 14, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Database references / Category: citation / Item: _citation.page_last / _citation.pdbx_database_id_DOI
Revision 1.4Jan 15, 2020Group: Other / Category: pdbx_database_status
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr
Revision 1.5Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.6Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EXCINUCLEASE ABC SUBUNIT
B: EXCINUCLEASE ABC SUBUNIT


Theoretical massNumber of molelcules
Total (without water)14,9032
Polymers14,9032
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)20 / 100MINIMAL ENERGY/VIOLATIONS
RepresentativeModel #1

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Components

#1: Protein EXCINUCLEASE ABC SUBUNIT


Mass: 7451.461 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN RESIDUES 618-673
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: PP3398 / Gene: UVRB / Plasmid: PNP118 / Gene (production host): UVRB(DOMAIN) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07025, UniProt: P0A8F8*PLUS
Compound detailsCHAIN A, B ARE THE UVRC-BINDING DOMAIN OF UVRB

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N-EDITED HSQC-NOESY
12113C-EDITED HSQC-NOESY
13113C/12C-FILTERED NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED PROTEIN. INTERMOLECULAR DISTANCE RESTRAINTS WERE OBTAINED

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Sample preparation

DetailsContents: 1 MM PROTEIN
Sample conditionsIonic strength: 0.2 M / pH: 7.5 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLORstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: SIMULATED ANNEALING PROTOCOL WITH NON-CRYSTALLOGRAPHIC SYMMETRY RESTRAINTS
NMR ensembleConformer selection criteria: MINIMAL ENERGY/VIOLATIONS / Conformers calculated total number: 100 / Conformers submitted total number: 20

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