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- PDB-2kpj: Solution Structure Of Protein SOS-response transcriptional repres... -

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Basic information

Entry
Database: PDB / ID: 2kpj
TitleSolution Structure Of Protein SOS-response transcriptional repressor, LexA From Eubacterium rectale. Northeast Structural Genomics Consortium Target ErR9A
ComponentsSOS-response transcriptional repressor, LexA
KeywordsTRANSCRIPTION REGULATOR / NESG / GFT / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


membrane => GO:0016020 / serine-type endopeptidase activity / DNA binding
Similarity search - Function
Peptidase S26A, signal peptidase I, serine active site / Signal peptidases I serine active site. / LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains ...Peptidase S26A, signal peptidase I, serine active site / Signal peptidases I serine active site. / LexA-like / Peptidase S24/S26A/S26B/S26C / Peptidase S24-like / LexA/Signal peptidase-like superfamily / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
SOS-response transcriptional repressor, LexA
Similarity search - Component
Biological speciesEubacterium rectale ATCC 33656 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWu, Y. / Eletsky, A. / Lee, D. / Ghosh, A. / Buchwald, W. / Zhang, Q. / Janjua, H. / Garcia, E. / Nair, R. / Sukumaran, D. ...Wu, Y. / Eletsky, A. / Lee, D. / Ghosh, A. / Buchwald, W. / Zhang, Q. / Janjua, H. / Garcia, E. / Nair, R. / Sukumaran, D. / Rost, B. / Acton, T. / Xiao, R. / Everett, J. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution Structure Of Protein SOS-response transcriptional repressor, LexA From Eubacterium rectale. Northeast Structural Genomics Consortium Target ErR9A
Authors: Wu, Y. / Eletsky, A. / Lee, D. / Ghosh, A. / Buchwald, W. / Zhang, Q. / Janjua, H. / Garcia, E. / Nair, R. / Sukumaran, D. / Rost, B. / Acton, T. / Everett, J. / Montelione, G.T. / Szyperski, T.
History
DepositionOct 16, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Database references / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _struct_ref_seq_dif.details
Revision 1.3Jun 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 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SOS-response transcriptional repressor, LexA


Theoretical massNumber of molelcules
Total (without water)10,7231
Polymers10,7231
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein SOS-response transcriptional repressor, LexA


Mass: 10723.237 Da / Num. of mol.: 1 / Fragment: sequence database residues 1-86
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium rectale ATCC 33656 (bacteria)
Strain: ATCC 33656 / VPI 0990 / Gene: EUBREC_1258 / Production host: Escherichia coli (E. coli) / References: UniProt: C4Z801

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1314,3D, GFT HNNCABCA
1414,3D, GFT CABCACONNH
1514,3D, GFT (H)CCH COSY
1613D, 15N-13C RESOLVEDSIMULTANIOUS NOESY
1713D HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
11.0 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM [U-5% 13C; U-100% 15N] protein, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.0 mMprotein-1[U-100% 13C; U-100% 15N]1
1.0 mMprotein-2[U-5% 13C; U-100% 15N]2
Sample conditionsIonic strength: 0.2 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker DMXBrukerDMX8002
Bruker DMXBrukerDMX8003

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Processing

NMR software
NameDeveloperClassification
AutoAssignZimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
AutoStructureHuang, Tejero, Powers and Montelionestructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PSVSBhattacharya and Montelionerefinement
TALOSCornilescu, Delaglio and Baxrefinement
XEASYBartels et al.data analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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