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- PDB-1i4v: SOLUTION STRUCTURE OF THE UMUD' HOMODIMER -

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Basic information

Entry
Database: PDB / ID: 1i4v
TitleSOLUTION STRUCTURE OF THE UMUD' HOMODIMER
ComponentsUMUD' PROTEIN
KeywordsHYDROLASE / SOS response / SOS mutagenesis / DNA repair / DNA polymerase V / DNA polymerase accessory protein / LexA repressor / lambda CI / signal peptidase / serine-lysine dyad / autocatalytic cleavage / serine protease
Function / homology
Function and homology information


DNA polymerase V complex / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / SOS response / ATP-dependent activity, acting on DNA / translesion synthesis / serine-type peptidase activity / single-stranded DNA binding / nucleic acid binding / DNA-directed DNA polymerase activity / DNA repair ...DNA polymerase V complex / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / SOS response / ATP-dependent activity, acting on DNA / translesion synthesis / serine-type peptidase activity / single-stranded DNA binding / nucleic acid binding / DNA-directed DNA polymerase activity / DNA repair / DNA damage response / regulation of DNA-templated transcription / proteolysis / DNA binding / identical protein binding
Similarity search - Function
Peptidase S24, LexA-like / Umud Fragment, subunit A / Umud Fragment, subunit A / LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Protein UmuD / Protein UmuD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsFerentz, A.E. / Walker, G.C. / Wagner, G.
CitationJournal: EMBO J. / Year: 2001
Title: Converting a DNA damage checkpoint effector (UmuD2C) into a lesion bypass polymerase (UmuD'2C).
Authors: Ferentz, A.E. / Walker, G.C. / Wagner, G.
History
DepositionFeb 23, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: 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 22, 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: UMUD' PROTEIN
B: UMUD' PROTEIN


Theoretical massNumber of molelcules
Total (without water)24,6182
Polymers24,6182
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations,structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein UMUD' PROTEIN


Mass: 12308.985 Da / Num. of mol.: 2 / Mutation: G25A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: UMUD / Plasmid: PET5A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS
References: UniProt: P04153, UniProt: P0AG11*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNHA
1213D 15N-separated NOESY
1332D NOESY
1442D NOESY
1523D 13C-separated NOESY
1663D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9 mM UmuD' U-15N; 150 mM NaCl, 10 mM phosphate, pH 6.0, 1mM DTT, 0.1 mM EDTA95% H2O/5% D2O
21.3 mM UmuD' U-15N,13C; 150 mM NaCl, 20 mM phosphate, pH 6.0, 1 mM DTT, 0.1 mM EDTA95% H2O/5% D2O
31.5 mM UmuD' unlabeled; 150 mM NaCl, 20 mM phosphate, pH 6.0, 1 mM DTT, 0.1 mM EDTA95% H20, 5% D2O
41.4 mM UmuD' unlabeled; 150 mM NaCl, 20 mM phosphate, pH 6.0, 1 mM DTT, 0.1 mM EDTA100% D2O
50.5 mM UmuD' U-10% 13C; 150 mM NaCl, 20 mM phosphate, pH 6.0, 1 mM DTT, 0.1 mM EDTA100% D2O
62.7 mM UmuD' U-100% 2H,15N and 2.7 mM unlabeled UmuD'; 150 mM NaCl, 20 mM phosphate, pH 6.0, 1 mM DTT, 0.1 mM EDTA95% H20, 5% D2O
Sample conditionsIonic strength: 150 mM NaCl / pH: 6.0 / Pressure: ambient / Temperature: 303 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
Varian UNITYPLUSVarianUNITYPLUS7501
Varian UNITYPLUSVarianUNITYPLUS4002
Bruker AMXBrukerAMX6003
Bruker AMXBrukerAMX5004
Varian VXRVarianVXR5005

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Processing

NMR software
NameVersionDeveloperClassification
Felix97Molecular Simulations Inc.processing
XEASY1.3.9Bartels et aldata analysis
X-PLOR3.851Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations,structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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