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- PDB-2kmg: The structure of the KlcA and ArdB proteins show a novel fold and... -

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Basic information

Entry
Database: PDB / ID: 2kmg
TitleThe structure of the KlcA and ArdB proteins show a novel fold and antirestriction activity against Type I DNA restriction systems in vivo but not in vitro
ComponentsKlcA
KeywordsGENE REGULATION / KlcA / ArdB / NMR spectroscopy / Anti-restriction / Plasmid
Function / homologyAntirestriction protein / Antirestriction protein / Antirestriction domain superfamily / Antirestriction protein / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / KlcA
Function and homology information
Biological speciesBordetella pertussis (bacteria)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsSerfiotis-Mitsa, D. / Herbert, A.P. / Roberts, G.A. / Soares, D.C. / White, J.H. / Blakely, G.W. / Uhrin, D. / Dryden, D.T.F.
CitationJournal: Nucleic Acids Res. / Year: 2010
Title: The structure of the KlcA and ArdB proteins reveals a novel fold and antirestriction activity against Type I DNA restriction systems in vivo but not in vitro
Authors: Serfiotis-Mitsa, D. / Herbert, A.P. / Roberts, G.A. / Soares, D.C. / White, J.H. / Blakely, G.W. / Uhrin, D. / Dryden, D.T.F.
History
DepositionJul 28, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 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 1.4May 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KlcA


Theoretical massNumber of molelcules
Total (without water)15,6741
Polymers15,6741
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein KlcA


Mass: 15673.630 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: klcA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q08L07

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: NMR derived solution structure of KlcA
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D CBCANH
1413D HNCO
1513D HN(CA)CO
1613D HBHANH
1713D HBHA(CO)NH
1812D 1H-13C HSQC (Aromatic Selective)
1913D H(CCO)NH
11013D C(CCO)NH
11113D (H)CCH-TOCSY
11212D 1H-13C HSQC
11313D 1H-15N NOESY
11413D 1H-13C NOESY
11512D (HB)CB(CGCD)HD
11612D (HB)CB(CGCDCE)HE
1173T1
1183T2
1193Heteronuclear NOE
1202IPAP for RDC measurement
12112D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7mM [U-98% 13C; U-98% 15N] KlcA-1, 20mM [U-100% 2H] sodium acetate-2, 0.05% sodium azide-3, 90% H2O/10% D2O90% H2O/10% D2O
20.7mM [U-98% 15N] KlcA-4, 20mM [U-100% 2H] sodium acetate-5, 0.05% sodium azide-6, 6.25mg/mL Pf1 phage-7, 90% H2O/10% D2O90% H2O/10% D2O
30.7mM [U-98% 15N] KlcA-8, 20mM [U-100% 2H] sodium acetate-9, 0.05% sodium azide-10, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMKlcA-1[U-98% 13C; U-98% 15N]1
20 mMsodium acetate-2[U-100% 2H]1
0.05 %sodium azide-31
0.7 mMKlcA-4[U-98% 15N]2
20 mMsodium acetate-5[U-100% 2H]2
0.05 %sodium azide-62
6.25 mg/mLPf1 phage-72
0.7 mMKlcA-8[U-98% 15N]3
20 mMsodium acetate-9[U-100% 2H]3
0.05 %sodium azide-103
Sample conditionsIonic strength: 20 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin1.3Bruker Biospincollection
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CcpNmr Analysis1.0.15CCPNchemical shift assignment
CcpNmr Analysis1.0.15CCPNdata analysis
CcpNmr Analysis1.0.15CCPNpeak picking
Azara2.7Boucherprocessing
ProcheckNMR3.5Laskowski and MacArthurstructure validation
WHAT IFVriendstructure validation
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: torsion angle dynamics, 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 / Representative conformer: 1

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