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- PDB-2kwa: 1H, 13C and 15N backbone and side chain resonance assignments of ... -

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Basic information

Entry
Database: PDB / ID: 2kwa
Title1H, 13C and 15N backbone and side chain resonance assignments of the N-terminal domain of the histidine kinase inhibitor KipI from Bacillus subtilis
ComponentsKinase A inhibitor
KeywordsTRANSFERASE INHIBITOR / Bacterial signal transduction / KipI / histidine kinase inhibition / Bacillus subtilis
Function / homology
Function and homology information


5-oxoprolinase (ATP-hydrolysing) / 5-oxoprolinase (ATP-hydrolyzing) activity / sporulation resulting in formation of a cellular spore / protein kinase inhibitor activity / ATP binding
Similarity search - Function
KipI family / Carboxyltransferase domain, subdomain C and D / Carboxyltransferase domain, subdomain C and D / Allophanate hydrolase subunit 1 / Gyrase A; domain 2 - #40 / Gyrase A; domain 2 / Cyclophilin-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
5-oxoprolinase subunit B
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsHynson, R.M.G. / Kwan, A. / Jacques, D.A. / Mackay, J.P. / Trewhella, J.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: A Novel Structure of an Antikinase and its Inhibitor
Authors: Jacques, D.A. / Langley, D.B. / Hynson, R.M.G. / Whitten, A.E. / Kwan, A. / Guss, J.M. / Trewhella, J.
History
DepositionMar 31, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kinase A inhibitor


Theoretical massNumber of molelcules
Total (without water)11,5661
Polymers11,5661
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Kinase A inhibitor / KipI-N / Sporulation inhibitor kipI


Mass: 11565.928 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: kipI / Production host: Escherichia coli (E. coli) / References: UniProt: P60495

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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 HN(CA)CB
1313D CBCA(CO)NH
1413D HNCO
1513D HN(CO)CA
1613D HNCA
1713D HN(CA)CO
1812D 1H-13C HSQC
1913D HBHA(CO)NH
11013D CC(CO)NH TOCSY
11113D 1H-15N TOCSY
11213D (H)CCH-TOCSY
11312D 1H-1H NOESY
11412D 1H-1H COSY
11513D 1H-1H TOCSY
1161HBCBCGCEHE
1171(HB)CB(CGCD)HD
11813D 1H-15N NOESY
11913D 1H-13C NOESY

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Sample preparation

DetailsContents: 1mM [U-100% 15N] KipI-N-1, 1mM [U-100% 13C; U-100% 15N] KipI-N-2, 1mM KipI-N-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMKipI-N-1[U-100% 15N]1
1 mMKipI-N-2[U-100% 13C; U-100% 15N]1
1 mMKipI-N-31
Sample conditionsIonic strength: 0.2 / pH: 6.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1-2.5Bruker Biospindata analysis
TopSpin2.1-2.5Bruker Biospincollection
SparkyGoddarddata analysis
SparkyGoddardchemical shift assignment
ARIALinge, O'Donoghue and Nilgeschemical shift assignment
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
Details: Heating and cooling steps changed from 10000, 5000 & 4000 to 20000, 20000 & 16000
NMR constraintsProtein phi angle constraints total count: 68 / Protein psi angle constraints total count: 68
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 0 ° / Representative conformer: 1 / Torsion angle constraint violation method: ARIA 2.1

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