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- PDB-2kjf: The solution structure of the circular bacteriocin carnocyclin A ... -

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Basic information

Entry
Database: PDB / ID: 2kjf
TitleThe solution structure of the circular bacteriocin carnocyclin A (CclA)
ComponentsCarnocyclin-A
KeywordsANTIMICROBIAL PROTEIN / circular bacteriocin / antimicrobial peptide / helical / saposin-fold / Antibiotic / Antimicrobial / Bacteriocin
Function / homology
Function and homology information


cytolysis / defense response to Gram-positive bacterium / extracellular region
Similarity search - Function
Bacteriocin AS-48 / Bacteriocin AS-48 / Circular bacteriocin / Bacteriocin class IId cyclical uberolysin-like / Bacteriocin As-48; Chain A / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesCarnobacterium maltaromaticum (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsMartin-Visscher, L.A. / Gong, X. / Duszyk, M. / Vederas, J.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: The three-dimensional structure of carnocyclin A reveals that many circular bacteriocins share a common structural motif.
Authors: Martin-Visscher, L.A. / Gong, X. / Duszyk, M. / Vederas, J.C.
History
DepositionMay 28, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carnocyclin-A


Theoretical massNumber of molelcules
Total (without water)5,8851
Polymers5,8851
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Carnocyclin-A


Mass: 5885.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Carnobacterium maltaromaticum (bacteria) / Strain: UAL307 / References: UniProt: B2MVM5

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HN(CA)CB
1413D CBCA(CO)NH
1513D 1H-15N NOESY
1613D 1H-15N TOCSY
1713D HNHA
1822D 1H-1H TOCSY
1922D 1H-1H COSY
11022D 1H-1H NOESY
11122D 1H-13C HSQC
11223D (H)CCH-TOCSY
11323D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-99% 13C; U-99% 15N] Carnocyclin A, 20 mM sodium phosphate, 1 mM EDTA, 1 mM sodium azide, 0.1 mM DSS, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-99% 13C; U-99% 15N] Carnocyclin A, 20 mM sodium phosphate, 1 mM EDTA, 1 mM sodium azide, 0.1 mM DSS, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMCarnocyclin A[U-99% 13C; U-99% 15N]1
20 mMsodium phosphate1
1 mMEDTA1
1 mMsodium azide1
0.1 mMDSS1
1 mMCarnocyclin A[U-99% 13C; U-99% 15N]2
20 mMsodium phosphate2
1 mMEDTA2
1 mMsodium azide2
0.1 mMDSS2
Sample conditionspH: 5.9 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, P. et al.refinement
CYANA2.1Guntert, P. et al.structure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 657 / NOE intraresidue total count: 209 / NOE long range total count: 125 / NOE medium range total count: 144 / NOE sequential total count: 179
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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