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Yorodumi- PDB-4hv7: Structure of ricin A chain bound with N-(N-(pterin-7-yl)carbonylg... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hv7 | ||||||
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Title | Structure of ricin A chain bound with N-(N-(pterin-7-yl)carbonylglycyl)glycine | ||||||
Components | Ricin | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / RICIN / PROTEIN-LIGAND COMPLEX / PTERIN / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / TOXIN / HYDROLASE / RIBOSOME-INACTIVATING PROTEIN / N-GLYCOSIDASE | ||||||
Function / homology | Function and homology information rRNA N-glycosylase / rRNA N-glycosylase activity / AMP binding / defense response / toxin activity / carbohydrate binding / killing of cells of another organism / negative regulation of translation Similarity search - Function | ||||||
Biological species | Ricinus communis (castor bean) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.869 Å | ||||||
Authors | Jasheway, K.R. / Monzingo, A.F. / Saito, R. / Pruet, J.M. / Manzano, L.A. / Wiget, P.A. / Anslyn, E.V. / Robertus, J.D. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Peptide-conjugated pterins as inhibitors of ricin toxin A. Authors: Saito, R. / Pruet, J.M. / Manzano, L.A. / Jasheway, K. / Monzingo, A.F. / Wiget, P.A. / Kamat, I. / Anslyn, E.V. / Robertus, J.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hv7.cif.gz | 74.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hv7.ent.gz | 53.6 KB | Display | PDB format |
PDBx/mmJSON format | 4hv7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hv7_validation.pdf.gz | 755.3 KB | Display | wwPDB validaton report |
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Full document | 4hv7_full_validation.pdf.gz | 757.4 KB | Display | |
Data in XML | 4hv7_validation.xml.gz | 15.2 KB | Display | |
Data in CIF | 4hv7_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/4hv7 ftp://data.pdbj.org/pub/pdb/validation_reports/hv/4hv7 | HTTPS FTP |
-Related structure data
Related structure data | 4huoC 4hupC 4hv3C 1rtcS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29936.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: castor bean / Source: (gene. exp.) Ricinus communis (castor bean) / Plasmid: PUTA / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P02879, rRNA N-glycosylase |
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#2: Chemical | ChemComp-19J / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-MLA / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.03 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 1.3 M ammonium sulfate, 0.1 M sodium malonate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 6, 2011 |
Radiation | Monochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.869→50 Å / Num. obs: 27776 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Rmerge(I) obs: 0.131 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 1.89→1.92 Å / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RTC Resolution: 1.869→48.99 Å / Occupancy max: 1 / Occupancy min: 0.15 / FOM work R set: 0.8074 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.985 Å2 / ksol: 0.329 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.74 Å2 / Biso mean: 30.792 Å2 / Biso min: 14.05 Å2
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Refinement step | Cycle: LAST / Resolution: 1.869→48.99 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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