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Yorodumi- PDB-2kux: Solution structure of the cyclotide kalata B5 from Oldenlandia affinis -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kux | ||||||
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Title | Solution structure of the cyclotide kalata B5 from Oldenlandia affinis | ||||||
Components | Kalata-B5 | ||||||
Keywords | PLANT PROTEIN / cyclotide / plant defense peptide / circular backbone / Disulfide bond / Knottin / Plant defense | ||||||
Function / homology | Cyclotide, bracelet, conserved site / Cyclotides bracelet subfamily signature. / Cyclotides profile. / Cyclotide / Cyclotide superfamily / Cyclotide family / defense response / Kalata-B5 Function and homology information | ||||||
Biological species | Oldenlandia affinis (plant) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Rosengren, K.J. / Craik, D.J. | ||||||
Citation | Journal: Biopolymers / Year: 2010 Title: Structural and biochemical characteristics of the cyclotide kalata B5 from Oldenlandia affinis Authors: Plan, M.R. / Rosengren, K.J. / Sando, L. / Daly, N.L. / Craik, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kux.cif.gz | 158.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kux.ent.gz | 135 KB | Display | PDB format |
PDBx/mmJSON format | 2kux.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kux_validation.pdf.gz | 337 KB | Display | wwPDB validaton report |
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Full document | 2kux_full_validation.pdf.gz | 408.2 KB | Display | |
Data in XML | 2kux_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 2kux_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/2kux ftp://data.pdbj.org/pub/pdb/validation_reports/ku/2kux | HTTPS FTP |
-Related structure data
Similar structure data |
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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/peptide | Mass: 3086.605 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oldenlandia affinis (plant) / References: UniProt: P58456 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: NMR solution structure of backbone cyclic plant peptide kalata B5. This peptide is head-to-tail cyclic, i.e. has a peptide bond between the N and C terminus. | ||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1-2mM Kalata-B5, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O |
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Sample | Units: mM / Component: Kalata-B5 / Conc. range: 1-2 |
Sample conditions | Ionic strength: 0 / pH: 5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 Details: Structures were calculated using torsion angle dynamics and subsequently refined by cartesian coordinate dynamics and powell minimization in explicit solvent using CNS. | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 50 / Conformers submitted total number: 20 / Representative conformer: 1 |