+Open data
-Basic information
Entry | Database: PDB / ID: 2mdv | ||||||
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Title | NMR structure of beta alpha alpha 38 | ||||||
Components | Designed protein | ||||||
Keywords | DE NOVO PROTEIN / Hub-linked / RHH1 Superfamily / Miniprotein | ||||||
Biological species | artificial gene (others) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Model details | lowest energy, model1 | ||||||
Authors | Kier, B.L. / Sheffler, W. / Baker, D. | ||||||
Citation | Journal: To be Published Title: Covalent Assembly of Homooligomeric Proteins Using Structure-templating Hubs Authors: Kier, B.L. / Sheffler, W. / Baker, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2mdv.cif.gz | 790.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2mdv.ent.gz | 689.1 KB | Display | PDB format |
PDBx/mmJSON format | 2mdv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2mdv_validation.pdf.gz | 375.2 KB | Display | wwPDB validaton report |
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Full document | 2mdv_full_validation.pdf.gz | 786.2 KB | Display | |
Data in XML | 2mdv_validation.xml.gz | 75 KB | Display | |
Data in CIF | 2mdv_validation.cif.gz | 112.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/md/2mdv ftp://data.pdbj.org/pub/pdb/validation_reports/md/2mdv | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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Details | Dimerization is covalent, via a WXCXW hub.) |
-Components
#1: Protein/peptide | Mass: 4599.339 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) artificial gene (others) |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: A beta-alpha-alpha dimer motif held together by a WXCXW hub, and employing the key features of the RHH1 superfamily. Designed & optimized using Foldit. | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 50 mM sodium phosphate, 0.5 mM DSS, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | |||||||||
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Sample |
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Sample conditions | Ionic strength: 0.11 / pH: 5 / Pressure: ambient / Temperature: 280 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 700 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||||||
NMR constraints | NOE constraints total: 1136 / NOE intraresidue total count: 654 / NOE long range total count: 44 / NOE medium range total count: 144 / NOE sequential total count: 284 / Disulfide bond constraints total count: 2 | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 40 / Conformers submitted total number: 32 |