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Yorodumi- PDB-2kdm: NMR structures of GA95 and GB95, two designed proteins with 95% s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2kdm | ||||||
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Title | NMR structures of GA95 and GB95, two designed proteins with 95% sequence identity but different folds and functions | ||||||
Components | DESIGNED PROTEIN | ||||||
Keywords | IgG binding protein / evolution / folding / protein design | ||||||
Function / homology | Ubiquitin-like (UB roll) - #10 / Ubiquitin-like (UB roll) / Roll / Alpha Beta Function and homology information | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | He, Y. / Alexander, P. / Chen, Y. / Bryan, P. / Orban, J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: From the Cover: A minimal sequence code for switching protein structure and function. Authors: Alexander, P.A. / He, Y. / Chen, Y. / Orban, J. / Bryan, P.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kdm.cif.gz | 355.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kdm.ent.gz | 296.9 KB | Display | PDB format |
PDBx/mmJSON format | 2kdm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kdm_validation.pdf.gz | 338.1 KB | Display | wwPDB validaton report |
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Full document | 2kdm_full_validation.pdf.gz | 467.9 KB | Display | |
Data in XML | 2kdm_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 2kdm_validation.cif.gz | 32.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/2kdm ftp://data.pdbj.org/pub/pdb/validation_reports/kd/2kdm | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 6363.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: designed protein |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.15-0.3 mM [U-100% 13C; U-100% 15N] Gb95, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O |
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Sample | Units: mM / Component: Gb95 / Isotopic labeling: [U-100% 13C; U-100% 15N] / Conc. range: 0.15-0.3 |
Sample conditions | Ionic strength: 100 / pH: 7.2 / Pressure: ambient / Temperature: 293 K |
-NMR measurement
NMR spectrometer | Type: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with acceptable covalent geometry Conformers calculated total number: 300 / Conformers submitted total number: 20 |