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- PDB-7pq4: NMR Structure of RgpB C-terminal Domain -

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Basic information

Entry
Database: PDB / ID: 7pq4
TitleNMR Structure of RgpB C-terminal Domain
ComponentsArginine-specific cysteine proteinase (Arg-gingipain)
KeywordsPROTEIN TRANSPORT / T9SS / Ig-like / gingipain / CTD
Function / homology
Function and homology information


cysteine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Peptidase M60, C-terminal / Peptidase M60 C-terminal domain / Peptidase C25, Ig-like domain / Gingipain propeptide / Gingipain, N-terminal superfamily / Gingipain propeptide superfamily / Gingipain, N-terminal / Peptidase family C25, C terminal ig-like domain / Propeptide_C25 / Gingipain ...Peptidase M60, C-terminal / Peptidase M60 C-terminal domain / Peptidase C25, Ig-like domain / Gingipain propeptide / Gingipain, N-terminal superfamily / Gingipain propeptide superfamily / Gingipain, N-terminal / Peptidase family C25, C terminal ig-like domain / Propeptide_C25 / Gingipain / Peptidase family C25 / Secretion system C-terminal sorting domain / Caspase-like domain superfamily / Immunoglobulin E-set / Immunoglobulin-like fold
Similarity search - Domain/homology
Arginine-specific cysteine proteinase (Arg-gingipain)
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsDorgan, B.J. / Curtis, M.A. / Garnett, J.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Queen Mary University of London United Kingdom
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Structural Model of a Porphyromonas gingivalis type IX Secretion System Shuttle Complex.
Authors: Dorgan, B. / Liu, Y. / Wang, S. / Aduse-Opoku, J. / Whittaker, S.B. / Roberts, M.A.J. / Lorenz, C.D. / Curtis, M.A. / Garnett, J.A.
History
DepositionSep 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 10, 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_PubMed / _citation.title / _citation_author.name
Revision 1.3Jun 19, 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

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Assembly

Deposited unit
A: Arginine-specific cysteine proteinase (Arg-gingipain)


Theoretical massNumber of molelcules
Total (without water)9,8541
Polymers9,8541
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7100 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein Arginine-specific cysteine proteinase (Arg-gingipain)


Mass: 9854.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Plasmid: pET46 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q51844

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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
121isotropic13D HNCO
131isotropic13D HN(CA)CO
141isotropic13D HN(CA)CB
151isotropic13D CBCA(CO)NH
161isotropic13D H(CCO)NH
171isotropic13D C(CO)NH
181isotropic13D (H)CCH-TOCSY
191isotropic13D CCH-TOCSY
1101isotropic1(HB)CB(CGCD)HD
1111isotropic1(HB)CB(CGCDCE)HE
1121isotropic13D 1H-13C NOESY
1131isotropic13D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-13C; U-15N] RgpB-CTD (G662-K736), 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM sodium azide, 90% H2O/10% D2O
Label: U-13C; U-15N / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMRgpB-CTD (G662-K736)[U-13C; U-15N]1
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
2 mMsodium azidenatural abundance1
Sample conditionsIonic strength: 70 mM / Label: condtions_1 / pH: 6 / Pressure: 1 atm / Temperature: 310 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
ARIA2.3Linge, O'Donoghue and Nilgesstructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
DANGLE1.1.1Cheung, Maguire, Stevens and Broadhurstgeometry optimization
WHAT IFVrienddata analysis
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 20 / Conformers submitted total number: 20

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