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- PDB-6sjw: Structure of the self-processing module of iron-regulated FrpC of... -

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Basic information

Entry
Database: PDB / ID: 6sjw
TitleStructure of the self-processing module of iron-regulated FrpC of N. Meningitidis with calcium ions
ComponentsIron-regulated protein FrpC
KeywordsMETAL BINDING PROTEIN / Repeat in toxin proteins / calcium
Function / homology
Function and homology information


cell outer membrane / toxin activity / calcium ion binding / extracellular region
Similarity search - Function
Haemolysin-type calcium binding-related / Haemolysin-type calcium binding protein related domain / RTX toxin determinant A / TSP type-3 repeat / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Serralysin-like metalloprotease, C-terminal
Similarity search - Domain/homology
Iron-regulated protein FrpC
Similarity search - Component
Biological speciesNeisseria meningitidis NM95 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsKuban, V. / Macek, P. / Hritz, J. / Nechvatalova, K. / Nedbalcova, K. / Faldyna, M. / Zidek, L. / Bumba, L.
Funding support Czech Republic, 6items
OrganizationGrant numberCountry
Grant Agency of the Czech Republic19-15175S Czech Republic
European Regional Development FundCZ.1.05/1.1.00/02.0068 Czech Republic
Other governmentLM2015042 Czech Republic
Other privateLM2015064 Czech Republic
Other privateLM2015043 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLQ1601 Czech Republic
CitationJournal: Mbio / Year: 2020
Title: Structural Basis of Ca 2+ -Dependent Self-Processing Activity of Repeat-in-Toxin Proteins.
Authors: Kuban, V. / Macek, P. / Hritz, J. / Nechvatalova, K. / Nedbalcova, K. / Faldyna, M. / Sebo, P. / Zidek, L. / Bumba, L.
History
DepositionAug 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 30, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.3Jun 23, 2021Group: Data collection / Category: pdbx_nmr_spectrometer / Item: _pdbx_nmr_spectrometer.field_strength
Revision 1.4Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Iron-regulated protein FrpC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1745
Polymers19,0141
Non-polymers1604
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area90 Å2
ΔGint-13 kcal/mol
Surface area9170 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1medoid

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Components

#1: Protein Iron-regulated protein FrpC


Mass: 19013.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis NM95 (bacteria) / Gene: frpC / Plasmid: pSPM-His / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): BL21(lambdaDE3) / References: UniProt: P55127
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HNCO
121isotropic13D HN(CA)CB
131isotropic13D CBCA(CO)NH
141isotropic13D 1H-15N NOESY
151isotropic13D (H)CCH-TOCSY
161isotropic13D 1H-13C NOESY aromatic
171isotropic22D 1H-13C HSQC aromatic
191isotropic315N R2
181isotropic315N R1
1101isotropic32D 1H-15N HSQC
1111isotropic32D ssNOE
1161isotropic43D 1H-13C NOESY aliphatic
2151isotropic32D 1H-15N HSQC
2141isotropic33D HN(CO)CA
2131isotropic33D HNCA
2121isotropic43D HN(CA)CB
2171isotropic43D CBCA(CO)NH

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Sample preparation

DetailsType: solution
Contents: 5 mM TRIS, 50 mM sodium chloride, 0.1 % sodium azide, 10 mM Calcium chloride, 0.5 mM [U-99% 13C; U-99% 15N] Self-processing module of FrpC, 90% H2O/10% D2O
Label: SPM / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
5 mMTRISnatural abundance1
50 mMsodium chloridenatural abundance1
0.1 %sodium azidenatural abundance1
10 mMCalcium chloridenatural abundance1
0.5 mMSelf-processing module of FrpC[U-99% 13C; U-99% 15N]1
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
165 mMspm-structured-303K7.4 1 atm303.2 K
265 mMspm-structured-283K7.4 1 atm283.2 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III7002
Bruker AVANCE IIIBrukerAVANCE III8503
Bruker AVANCE IIIBrukerAVANCE III9504

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.115Goddardchemical shift assignment
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
GROMACS5.1.1Erik Lindahl, David van der Spoel, Berk Hess, Mark Abrahamrefinement
TopSpin3.2Bruker Biospincollection
Sparky3.115Goddarddata analysis
Sparky3.115Goddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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