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- PDB-8u9o: Solution structure of RsgI9 CRE domain from C. thermocellum -

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Basic information

Entry
Database: PDB / ID: 8u9o
TitleSolution structure of RsgI9 CRE domain from C. thermocellum
Components(Anti-sigma-I factor RsgI9) x 2
KeywordsSIGNALING PROTEIN / RsgI / Cellulosome / Anti-sigma factor / auto-proteolysis
Function / homologyAnti-sigma factor RsgI, N-terminal / Anti-sigma factor N-terminus / RsgI N-terminal anti-sigma domain profile. / Peptidase S1C / membrane => GO:0016020 / serine-type endopeptidase activity / Peptidase S1, PA clan / plasma membrane / Anti-sigma-I factor RsgI9
Function and homology information
Biological speciesAcetivibrio thermocellus DSM 1313 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsTakayesu, A. / Mahoney, B.J. / Clubb, R.T.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FC02-02ER63421 United States
CitationJournal: Proteins / Year: 2024
Title: Insight into the autoproteolysis mechanism of the RsgI9 anti-sigma factor from Clostridium thermocellum.
Authors: Takayesu, A. / Mahoney, B.J. / Goring, A.K. / Jessup, T. / Ogorzalek Loo, R.R. / Loo, J.A. / Clubb, R.T.
History
DepositionSep 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anti-sigma-I factor RsgI9
B: Anti-sigma-I factor RsgI9


Theoretical massNumber of molelcules
Total (without water)20,0382
Polymers20,0382
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR relaxation study, NMR relaxation parameters consistent with intact monomer, gel filtration, Single peak in chromatogram corresponding to both fragments of autoproteolyzed sample
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Anti-sigma-I factor RsgI9


Mass: 2376.539 Da / Num. of mol.: 1 / Fragment: UNP residues 167-188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio thermocellus DSM 1313 (bacteria)
Gene: rsgI9, Cthe_0260 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A3DC20
#2: Protein Anti-sigma-I factor RsgI9


Mass: 17661.021 Da / Num. of mol.: 1 / Fragment: UNP residues 189-343
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio thermocellus DSM 1313 (bacteria)
Gene: rsgI9 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A3DC20

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N TROSY
222isotropic22D 1H-13C HSQC aliphatic
232isotropic22D 1H-13C HSQC aromatic
242isotropic22D 1H-1H TOCSY
252isotropic22D 1H-1H COSY
161isotropic23D HNCO
171isotropic23D HN(CA)CO
181isotropic23D HNCA
191isotropic23D HN(COCA)CB
1101isotropic23D HN(CA)CB
2112isotropic23D (H)CCH-COSY
1121isotropic23D HNHA
1131isotropic23D 1H-15N NOESY
2142isotropic13D 1H-13C NOESY aliphatic
1151isotropic13D 1H-13C NOESY aliphatic
1161isotropic11H-15N heteronoe

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution1200 uM [U-13C; U-15N] RsgI9 CRE, 0.03 % sodium azide, 50 mM sodium phosphate, 200 mM sodium chloride, 8 % [U-2H] D2O, 93% H2O/7% D2O13C 15N sample, water93% H2O/7% D2O
solution2200 uM [U-13C; U-15N] RsgI9 CRE, 0.03 % sodium azide, 50 mM sodium phosphate, 200 mM sodium chloride, 100 % [U-2H] d2o, 100% D2O13C 15N sample, D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
200 uMRsgI9 CRE[U-13C; U-15N]1
0.03 %sodium azidenatural abundance1
50 mMsodium phosphatenatural abundance1
200 mMsodium chloridenatural abundance1
8 %D2O[U-2H]1
200 uMRsgI9 CRE[U-13C; U-15N]2
0.03 %sodium azidenatural abundance2
50 mMsodium phosphatenatural abundance2
200 mMsodium chloridenatural abundance2
100 %d2o[U-2H]2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
1200 mM13C 15N sample, water6.0 1 atm298 K
2200 mM13C 15N sample, D2O6.0 1 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE III HDBrukerAVANCE III HD6001
Bruker AVANCE NEOBrukerAVANCE NEO8002

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH3.6Schwieters, Kuszewski, Tjandra and Clorestructure calculation
Xipp1.21.7Daniel S. Garrett, Mengli Cai, and G. Marius Clorechemical shift assignment
Xipp1.21.7Daniel S. Garrett, Mengli Cai, and G. Marius Clorepeak picking
CARAKeller and Wuthrichchemical shift assignment
TopSpinBruker Biospincollection
TopSpinBruker Biospindata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MOLMOLKoradi, Billeter and Wuthrichrefinement
TALOS-NYang Shen and Ad Baxgeometry optimization
PROCHECK / PROCHECK-NMRLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorntonrefinement
UNIOPedro Serrano, Bill Pedrini, Biswaranjan Mohanty, Michael Geralt, Torsten Herrmann, and Kurt Wuthrichpeak picking
NMRFAM-SPARKYWoonghee Lee, Marco Tonelli, and John L. Markleydata analysis
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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