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- PDB-6sjx: Precursor structure of the self-processing module of iron-regulat... -

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Basic information

Entry
Database: PDB / ID: 6sjx
TitlePrecursor structure 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 serogroup C (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
Revision 1.5Jun 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: Iron-regulated protein FrpC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4476
Polymers19,2471
Non-polymers2005
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area350 Å2
ΔGint-49 kcal/mol
Surface area9390 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / 20structures with the least restraint violations
RepresentativeModel #1medoid

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Components

#1: Protein Iron-regulated protein FrpC


Mass: 19246.879 Da / Num. of mol.: 1 / Mutation: P415A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup C (bacteria)
Gene: frpC / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P55127
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / 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
111isotropic12D 1H-15N HSQC
121isotropic13D HNCO
131isotropic13D HN(CA)CB
141isotropic13D CBCA(CO)NH
151isotropic13D (H)CCH-TOCSY
161isotropic23D 1H-13C NOESY aliphatic
171isotropic23D 1H-15N NOESY
282isotropic31D WATERGATE W5

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution15 mM TRIS, 50 mM sodium chloride, 0.1 % sodium azide, 10 mM Calcium chloride, 0.35 mM [U-99% 13C; U-99% 15N] P415A mutant of Self-processing module of FrpC, 90% H2O/10% D2OGSDP415A-SPM90% H2O/10% D2O
solution250 mM TRIS, 50 mM sodium chloride, 0.1 % sodium azide, 0.707 mM P415A mutant of Self-processing module of FrpC, 90% H2O/10% D2Otitration - GSDP415A-SPM90% H2O/10% D2OThe sample was dialysed overnight against a CaCl2-free buffer. The sample was titrated with the solution of 50 mM disodium EDTA, 50 mM NaCl, 50 mM Tris, and pH 7.4.
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
5 mMTRISnatural abundance1
50 mMsodium chloridenatural abundance1
0.1 %sodium azidenatural abundance1
10 mMCalcium chloridenatural abundance1
0.35 mMP415A mutant of Self-processing module of FrpC[U-99% 13C; U-99% 15N]1
50 mMTRISnatural abundance2
50 mMsodium chloridenatural abundance2
0.1 %sodium azidenatural abundance2
0.707 mMP415A mutant of Self-processing module of FrpCnatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
165 mMstructured-at-303K7.41 atm303.2 K
2100 mMtitration7.41 atm303.2 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8503
Bruker AVANCE IIIBrukerAVANCE III9502

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Processing

NMR software
NameVersionDeveloperClassification
Sparky3.115Goddardchemical shift assignment
TopSpin3.2Bruker Biospinprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
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: 5
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 20 / Conformers submitted total number: 14

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