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- PDB-2mz8: Solution NMR structure of Salmonella Typhimurium transcriptional ... -

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Basic information

Entry
Database: PDB / ID: 2mz8
TitleSolution NMR structure of Salmonella Typhimurium transcriptional regulator protein Crl
ComponentsSigma factor-binding protein Crl
KeywordsTRANSCRIPTION REGULATOR / Crl / Salmonella enterica / serovar Typhimurium / sigmaS / sigma factor binding protein / sigma factor activator / stationary phase / stress response / transcriptional regulator / curli / RpoS / RNA polymerase
Function / homology
Function and homology information


positive regulation of cellulose biosynthetic process / positive regulation of DNA-templated transcription / cytoplasm
Similarity search - Function
Sigma factor-binding protein Crl monomer / Sigma factor-binding transcriptional regulator Crl / Sigma factor-binding protein Crl superfamily / Sigma factor-binding transcriptional regulator Crl / TATA-Binding Protein / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Sigma factor-binding protein Crl
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsCavaliere, P. / Levi-Acobas, F. / Monteil, V. / Bellalou, J. / Mayer, C. / Norel, F. / Sizun, C.
CitationJournal: Sci Rep / Year: 2015
Title: Binding interface between the Salmonella sigma (S)/RpoS subunit of RNA polymerase and Crl: hints from bacterial species lacking crl.
Authors: Cavaliere, P. / Sizun, C. / Levi-Acobas, F. / Nowakowski, M. / Monteil, V. / Bontems, F. / Bellalou, J. / Mayer, C. / Norel, F.
History
DepositionFeb 7, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sigma factor-binding protein Crl


Theoretical massNumber of molelcules
Total (without water)18,1691
Polymers18,1691
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Sigma factor-binding protein Crl


Mass: 18169.443 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: crl, STM0319 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7CR52

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D 1H-15N NOESY
2312D 1H-15N HSQC
2422D 1H-15N HSQC
2523D HN(CA)CB
1622D 1H-15N HSQC
1723D HNCA
1823D HN(CO)CA
1923D CBCA(CO)NH
11023D HNCO
11142D 1H-15N HSQC
11243D HNCO
11343D HN(CA)CO
11443D HNCA
11543D HN(CO)CA
11632D 1H-13C HSQC
11733D (H)CCH-TOCSY
11833D 1H-13C NOESY
11932D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM [U-98% 15N] His_ST-Crl, 50.0 mM Sodium phosphate, 300.0 mM Sodium chloride, 2.0 mM Dithiotreitol, 93% H2O/7% D2O93% H2O/7% D2O
20.25 mM [U-98% 13C; U-98% 15N] His_ST-Crl, 50.0 mM Sodium phosphate, 300.0 mM Sodium chloride, 2.0 mM Dithiotreitol, 93% H2O/7% D2O93% H2O/7% D2O
30.35 mM [U-198% 13C; U-198% 15N] His_ST-Crl, 50.0 mM Sodium phosphate, 300.0 mM Sodium chloride, 2.0 mM Dithiotreitol, 100% D2O100% D2O
40.300 mM [U-100% 13C; U-100% 15N; U-80% 2H] His_ST-Crl, 50.000 mM Sodium phosphate, 300.000 mM Sodium chloride, 2.0 mM Dithiotreitol, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMHis_ST-Crl-1[U-98% 15N]1
50.0 mMSodium phosphate-21
300.0 mMSodium chloride-31
2.0 mMDithiotreitol-41
0.25 mMHis_ST-Crl-5[U-98% 13C; U-98% 15N]2
50.0 mMSodium phosphate-62
300.0 mMSodium chloride-72
2.0 mMDithiotreitol-82
0.35 mMHis_ST-Crl-9[U-198% 13C; U-198% 15N]3
50.0 mMSodium phosphate-103
300.0 mMSodium chloride-113
2.0 mMDithiotreitol-123
0.300 mMHis_ST-Crl-13[U-100% 13C; U-100% 15N; U-80% 2H]4
50.000 mMSodium phosphate-144
300.000 mMSodium chloride-154
2.0 mMDithiotreitol-164
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.300 8.000 1.000 atm293.000 K
20.300 6.500 1.000 atm293.000 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.2CCPNnmr data analysis
CYANA2.2L.A. Systemsnmr structure calculation
NMRPipe1NIDDKD NIHnmr data processing
TALOS-N1NIDDKD NIHdihedral angles
CYANArefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1607 / NOE intraresidue total count: 437 / NOE long range total count: 527 / NOE medium range total count: 238 / NOE sequential total count: 405 / Protein phi angle constraints total count: 105 / Protein psi angle constraints total count: 112
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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