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Yorodumi- PDB-2a00: The solution structure of the AMP-PNP bound nucleotide binding do... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a00 | ||||||
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Title | The solution structure of the AMP-PNP bound nucleotide binding domain of KdpB | ||||||
Components | Potassium-transporting ATPase B chain | ||||||
Keywords | HYDROLASE / ALPHA-BETA SANDWICH | ||||||
Function / homology | Function and homology information P-type K+ transporter / P-type potassium transmembrane transporter activity / potassium:proton antiporter complex / potassium ion-transporting ATPase complex / monoatomic cation transmembrane transport / potassium ion transmembrane transport / potassium ion transport / magnesium ion binding / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Haupt, M. / Bramkamp, M. / Coles, M. / Altendorf, K. / Kessler, H. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 Title: The Holo-form of the Nucleotide Binding Domain of the KdpFABC Complex from Escherichia coli Reveals a New Binding Mode Authors: Haupt, M. / Bramkamp, M. / Heller, M. / Coles, M. / Deckers-Hebestreit, G. / Herkenhoff-Hesselmann, B. / Altendorf, K. / Kessler, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a00.cif.gz | 888.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a00.ent.gz | 747.9 KB | Display | PDB format |
PDBx/mmJSON format | 2a00.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a00_validation.pdf.gz | 456.2 KB | Display | wwPDB validaton report |
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Full document | 2a00_full_validation.pdf.gz | 639.6 KB | Display | |
Data in XML | 2a00_validation.xml.gz | 108.8 KB | Display | |
Data in CIF | 2a00_validation.cif.gz | 128.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/2a00 ftp://data.pdbj.org/pub/pdb/validation_reports/a0/2a00 | HTTPS FTP |
-Related structure data
Related structure data | 2a29C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 17168.297 Da / Num. of mol.: 1 / Fragment: KdpBN, nucleotide binding domain of KdpB Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: kdpB / Plasmid: PET16B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03960, EC: 3.6.3.12 |
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#2: Chemical | ChemComp-ANP / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.0MM U-15N,13C KDPBN, 50MM phosphate buffer, 100MM NACL, 0.05% sodium azide, 15MM ATP- PNP; 1.0MM U-15N KDPBN, 50MM phosphate buffer, 100MM NACL, 0.05% sodium azide, 15MM AMP- PNP |
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Sample conditions | Ionic strength: 100mM NACL / pH: 6.0 / Pressure: AMBIENT / Temperature: 300 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: Based on a total of 1667 NOE-based distance restraints, 230 dihedral angle restraints and 21 intermolecular distance restraints | ||||||||||||||||
NMR representative | Selection criteria: lowest violations | ||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 50 / Conformers submitted total number: 19 |