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Yorodumi- PDB-2k0p: Determination of a Protein Structure in the Solid State from NMR ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2k0p | ||||||
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Title | Determination of a Protein Structure in the Solid State from NMR Chemical Shifts | ||||||
Components | Immunoglobulin G-binding protein G | ||||||
Keywords | PROTEIN BINDING / solid-state / chemical shift restraints / GB1 / Cell wall / IgG-binding protein / Peptidoglycan-anchor / Secreted | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus sp. group G (bacteria) | ||||||
Method | SOLID-STATE NMR / MD, MC hybrid refinment against Target Fuction weighted by chemical shift accuracy, a molecular mechanics force field | ||||||
Authors | Robustelli, P. / Cavalli, A. / Salvatella, X. / Vendruscolo, M. | ||||||
Citation | Journal: Structure / Year: 2008 Title: Determination of protein structures in the solid state from NMR chemical shifts. Authors: Robustelli, P. / Cavalli, A. / Vendruscolo, M. #1: Journal: Angew.Chem.Int.Ed.Engl. / Year: 2007 Title: Solid-state protein-structure determination with proton-detected triple-resonance 3D magic-angle-spinning NMR spectroscopy. Authors: Zhou, D.H. / Shea, J.J. / Nieuwkoop, A.J. / Franks, W.T. / Wylie, B.J. / Mullen, C. / Sandoz, D. / Rienstra, C.M. #2: Journal: J.Am.Chem.Soc. / Year: 2007 Title: Proton-detected solid-state NMR spectroscopy of fully protonated proteins at 40 kHz magic-angle spinning. Authors: Zhou, D.H. / Shah, G. / Cormos, M. / Mullen, C. / Sandoz, D. / Rienstra, C.M. #3: Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: Protein structure determination from NMR chemical shifts. Authors: Cavalli, A. / Salvatella, X. / Dobson, C.M. / Vendruscolo, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2k0p.cif.gz | 20.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2k0p.ent.gz | 12.8 KB | Display | PDB format |
PDBx/mmJSON format | 2k0p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2k0p_validation.pdf.gz | 244 KB | Display | wwPDB validaton report |
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Full document | 2k0p_full_validation.pdf.gz | 243.8 KB | Display | |
Data in XML | 2k0p_validation.xml.gz | 2.5 KB | Display | |
Data in CIF | 2k0p_validation.cif.gz | 2.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/2k0p ftp://data.pdbj.org/pub/pdb/validation_reports/k0/2k0p | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Antibody | Mass: 6228.809 Da / Num. of mol.: 1 / Fragment: GB1 / Mutation: T2Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus sp. group G (bacteria) / Gene: spg / Production host: Escherichia coli (E. coli) / References: UniProt: P06654 |
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-Experimental details
-Experiment
Experiment | Method: SOLID-STATE NMR Method details: Solid-state structure of Beta-1 Immunoglobulin binding domain of protein G (GB1) solved from Ha, Ca, Cb, and N backbone chemical shifts. | ||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: For Experimental Data See BMRB Entry 15156 |
-Sample preparation
Details | Contents: 10 mg/mL [U-100% 13C; U-100% 15N] GB1, 0.5 v/v Methyl Pentane diol, 0.25 v/v Isopropanol Solvent system: 0.5 v/v Methyl Pentane diol/0.25 v/v Isopropanol | ||||||||||||||||
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Sample |
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Sample conditions | Pressure: 1 atm / Temperature: 278 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: MD, MC hybrid refinment against Target Fuction weighted by chemical shift accuracy, a molecular mechanics force field Software ordinal: 1 Details: Structure Selection and Refinement were performed according to CHESHIRE protocol for calculation of structures from NMR Chemical Shifts (Cavalli et al., 2007, PNAS, 104, 9615-9620) | ||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 1500 / Conformers submitted total number: 1 |