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- PDB-2k0g: Solution Structure of a Bacterial Cyclic Nucleotide-Activated K+ ... -

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Basic information

Entry
Database: PDB / ID: 2k0g
TitleSolution Structure of a Bacterial Cyclic Nucleotide-Activated K+ Channel Binding Domain in Complex with cAMP
ComponentsMll3241 protein
KeywordsMEMBRANE PROTEIN / Ion Channel / helical bundle beta barrel core / Phosphate Binding Cassette with cAMP bound / Cyclic Nucleotide Binding Domain / Solution Structure
Function / homology
Function and homology information


potassium channel activity / cAMP binding / identical protein binding / plasma membrane
Similarity search - Function
Cyclic nucleotide-regulated ion channel, N-terminal / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls ...Cyclic nucleotide-regulated ion channel, N-terminal / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Ion transport domain / Ion transport protein / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / Cyclic nucleotide-gated potassium channel mll3241
Similarity search - Component
Biological speciesRhizobium loti (bacteria)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsSchunke, S. / Stoldt, M. / Willbold, D.
CitationJournal: Embo Rep. / Year: 2009
Title: Solution structure of the Mesorhizobium loti K1 channel cyclic nucleotide-binding domain in complex with cAMP.
Authors: Schunke, S. / Stoldt, M. / Novak, K. / Kaupp, U.B. / Willbold, D.
History
DepositionFeb 2, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mll3241 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3122
Polymers14,9831
Non-polymers3291
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 10015 structures with the lowest energy
RepresentativeModel #1lowest energy and fewest violations

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Components

#1: Protein Mll3241 protein


Mass: 14983.222 Da / Num. of mol.: 1
Fragment: Cyclic Nucleotide Binding Domain, residues 216-355
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium loti (bacteria) / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q98GN8
#2: Chemical ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP / Cyclic adenosine monophosphate


Mass: 329.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N5O6P

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1323D 13C-separated NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM [U-100% 13C; U-100% 15N] MlCNBD Protein, 0.5 mM [U-100% 13C; U-100% 15N] ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE, 95% H2O, 5% D2O95% H2O/5% D2O
20.5 mM [U-100% 13C; U-100% 15N] MlCNBD Protein, 0.5 mM [U-100% 13C; U-100% 15N] ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE, 100 % D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMMlCNBD Protein-1[U-100% 13C; U-100% 15N]1
0.5 mMADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE-2[U-100% 13C; U-100% 15N]1
0.5 mMMlCNBD Protein-3[U-100% 13C; U-100% 15N]2
0.5 mMADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE-4[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 100 mM KCl / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: VARIAN Unity INOVA with cryogenic triple resonance probe
Manufacturer: Varian / Model: Unity INOVA with cryogenic triple resonance probe / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ1.1dVarianprocessing
NMRPipe3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichpeak picking
ATNOS/CANDID1.1Herrmann, Guntert and Wuthrichstructure solution
ATNOS/CANDID1.1Herrmann, Guntert and Wuthrichrefinement
CYANA1.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA1.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: The NMR structure ensemble is based on total of 2388 NOE-derived distance constraints.
NMR constraintsNOE constraints total: 2388 / NOE intraresidue total count: 441 / NOE long range total count: 820 / NOE medium range total count: 477 / NOE sequential total count: 624
NMR representativeSelection criteria: lowest energy and fewest violations
NMR ensembleConformer selection criteria: 15 structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15

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