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Yorodumi- PDB-5kph: Solution NMR Structure of Denovo Beta Sheet Design Protein, North... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5kph | ||||||
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Title | Solution NMR Structure of Denovo Beta Sheet Design Protein, Northeast Structural Genomics Consortium (NESG) Target OR485 | ||||||
Components | De novo Beta Sheet Design Protein OR485 | ||||||
Keywords | DE NOVO PROTEIN / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG | ||||||
Biological species | synthetic construct (others) | ||||||
Method | SOLUTION NMR / simulated annealing, distance geometry, molecular dynamics | ||||||
Authors | Tang, Y. / Liu, G. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: Science / Year: 2017 Title: Principles for designing proteins with cavities formed by curved beta sheets. Authors: Marcos, E. / Basanta, B. / Chidyausiku, T.M. / Tang, Y. / Oberdorfer, G. / Liu, G. / Swapna, G.V. / Guan, R. / Silva, D.A. / Dou, J. / Pereira, J.H. / Xiao, R. / Sankaran, B. / Zwart, P.H. / ...Authors: Marcos, E. / Basanta, B. / Chidyausiku, T.M. / Tang, Y. / Oberdorfer, G. / Liu, G. / Swapna, G.V. / Guan, R. / Silva, D.A. / Dou, J. / Pereira, J.H. / Xiao, R. / Sankaran, B. / Zwart, P.H. / Montelione, G.T. / Baker, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5kph.cif.gz | 628.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kph.ent.gz | 535.2 KB | Display | PDB format |
PDBx/mmJSON format | 5kph.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5kph_validation.pdf.gz | 528.8 KB | Display | wwPDB validaton report |
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Full document | 5kph_full_validation.pdf.gz | 714.1 KB | Display | |
Data in XML | 5kph_validation.xml.gz | 44.6 KB | Display | |
Data in CIF | 5kph_validation.cif.gz | 55.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kp/5kph ftp://data.pdbj.org/pub/pdb/validation_reports/kp/5kph | HTTPS FTP |
-Related structure data
Related structure data | 5kpeC 5l33C 5tphC 5tpjC 5trvC 5ts4C 5u35C C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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Details | Monomer as determined by light scattering. |
-Components
#1: Protein | Mass: 10097.393 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 0.80 mM [U-99% 13C; U-99% 15N] OR485, 90% H2O/10% D2O Details: Low Salt, 5 mM DTT 100 mM NaCl 10 mM Tris-HCl pH 7.5 0.02 % NaN3, volume:0.3 mL; protein concentration:0.80 mM Label: OR485.004 / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 0.80 mM / Component: OR485 / Isotopic labeling: [U-99% 13C; U-99% 15N] |
Sample conditions | Details: Low Salt, 5 mM DTT 100 mM NaCl 10 mM Tris-HCl pH 7.5 0.02 % NaN3, volume:0.3 mL; protein concentration:0.80 mM Ionic strength: 100 mM / Ionic strength err: 1 / Label: conditions_1 / pH: 7.5 / PH err: 0.1 / Pressure: 1 atm / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.2 |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing, distance geometry, molecular dynamics Software ordinal: 1 | |||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |