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- PDB-8her: Solution structure of the periplasmic domain of RsgI6 from Clostr... -

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Basic information

Entry
Database: PDB / ID: 8her
TitleSolution structure of the periplasmic domain of RsgI6 from Clostridium thermocellum
Components(Anti-sigma factor) x 2
KeywordsSIGNALING PROTEIN / ANTI-SIGMA FACTOR / TRANSCRIPTION
Function / homology
Function and homology information


polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Anti-sigma factor RsgI, N-terminal / Anti-sigma factor N-terminus / RsgI N-terminal anti-sigma domain profile. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesAcetivibrio thermocellus DSM 1313 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsChen, C. / Feng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Sci Adv / Year: 2023
Title: Essential autoproteolysis of bacterial anti-sigma factor RsgI for transmembrane signal transduction.
Authors: Chen, C. / Dong, S. / Yu, Z. / Qiao, Y. / Li, J. / Ding, X. / Li, R. / Lin, J. / Bayer, E.A. / Liu, Y.J. / Cui, Q. / Feng, Y.
History
DepositionNov 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2May 15, 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:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)19,8182
Polymers19,8182
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2120 Å2
ΔGint-11 kcal/mol
Surface area8800 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Anti-sigma factor


Mass: 1158.325 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio thermocellus DSM 1313 (bacteria)
Gene: rsgI6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H6SHY0
#2: Protein Anti-sigma factor


Mass: 18660.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acetivibrio thermocellus DSM 1313 (bacteria)
Gene: rsgI6 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H6SHY0

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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 HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D HNCO
161isotropic13D HN(CA)CO
171isotropic13D HBHA(CO)NH
181isotropic13D HBHANH
191isotropic13D (H)CCH-TOCSY
1101isotropic13D (H)CCH-COSY
1111isotropic13D CCH-TOCSY
1121isotropic13D 1H-13C NOESY aliphatic
1131isotropic13D 1H-13C NOESY aromatic
1141isotropic13D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-100% 13C; U-100% 15N] RsgI6-PD, 50 mM sodium phosphate, 150 mM sodium chloride, 0.02 % w/v DSS, 100% D2O
Label: sample1 / Solvent system: 100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMRsgI6-PD[U-100% 13C; U-100% 15N]1
50 mMsodium phosphatenatural abundance1
150 mMsodium chloridenatural abundance1
0.02 % w/vDSSnatural abundance1
Sample conditionsIonic strength: 200 mM / Label: condition1 / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 600 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
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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