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Yorodumi- PDB-3hiw: Crystal structure of Saporin-L1 in complex with the cyclic tetran... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hiw | ||||||
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Title | Crystal structure of Saporin-L1 in complex with the cyclic tetranucleotide inhibitor, a transition state analogue | ||||||
Components | Vacuolar saporin | ||||||
Keywords | Hydrolase/Hydrolase inhibitor / transition state / ribosome inactivating proteins / RIPs / Hydrolase / Plant defense / Protein synthesis inhibitor / Toxin / Hydrolase-Hydrolase inhibitor COMPLEX | ||||||
Function / homology | Function and homology information rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / negative regulation of translation Similarity search - Function | ||||||
Biological species | Saponaria officinalis (common soapwort) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Ho, M. / Sturm, M.B. / Almo, S.C. / Schramm, V.L. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2009 Title: Transition state analogues in structures of ricin and saporin ribosome-inactivating proteins. Authors: Ho, M.C. / Sturm, M.B. / Almo, S.C. / Schramm, V.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hiw.cif.gz | 126.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hiw.ent.gz | 99.1 KB | Display | PDB format |
PDBx/mmJSON format | 3hiw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/3hiw ftp://data.pdbj.org/pub/pdb/validation_reports/hi/3hiw | HTTPS FTP |
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-Related 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
#1: Protein | Mass: 28767.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saponaria officinalis (common soapwort) Production host: Escherichia coli (E. coli) / References: UniProt: Q2QEH4 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.25 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 20% PEG2000MME, 0.1M sodium acetate, 0.4M potassium thiocyanate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 2, 2008 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→20 Å / Num. obs: 44853 / % possible obs: 97.1 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.041 / Χ2: 1.031 / Net I/σ(I): 18.983 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.64 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.65 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 63.23 Å2 / Biso mean: 17.906 Å2 / Biso min: 7.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.64 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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