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Yorodumi- PDB-3s9q: Crystal structure of native type 1 ribosome inactivating protein ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3s9q | ||||||
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Title | Crystal structure of native type 1 ribosome inactivating protein from Momordica balsamina at 1.67 A resolution | ||||||
Components | Ribosome inactivating proteinRibosome-inactivating protein | ||||||
Keywords | HYDROLASE / RIP / RNA N-glycosidase / Plant protein / GOL | ||||||
Function / homology | Function and homology information rRNA N-glycosylase / rRNA N-glycosylase activity / toxin activity / negative regulation of translation / nucleotide binding Similarity search - Function | ||||||
Biological species | Momordica balsamina (balsam apple) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å | ||||||
Authors | Pandey, N. / Kushwaha, G.S. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2012 Title: Crystal structures of a type-1 ribosome inactivating protein from Momordica balsamina in the bound and unbound states. Authors: Kushwaha, G.S. / Pandey, N. / Sinha, M. / Singh, S.B. / Kaur, P. / Sharma, S. / Singh, T.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s9q.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3s9q.ent.gz | 48.6 KB | Display | PDB format |
PDBx/mmJSON format | 3s9q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s9/3s9q ftp://data.pdbj.org/pub/pdb/validation_reports/s9/3s9q | HTTPS FTP |
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-Related structure data
Related structure data | 3n1nC 3rl9C 3sj6C 3u6zC 3v2kC 1ahaS 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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Unit cell |
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-Components
#1: Protein | Mass: 27093.756 Da / Num. of mol.: 1 / Fragment: A / Source method: isolated from a natural source / Source: (natural) Momordica balsamina (balsam apple) / References: UniProt: D9J2T9, rRNA N-glycosylase | ||
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#2: Sugar | ChemComp-NAG / | ||
#3: Chemical | #4: 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: 2.43 Å3/Da / Density % sol: 49.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 14% PEG6000, 0.1M Sodium Phosphate , pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 23, 2009 / Details: mirrir |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.67→65.09 Å / Num. all: 26840 / Num. obs: 26840 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 16.7 Å2 / Rsym value: 0.107 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.67→1.7 Å / Mean I/σ(I) obs: 2.2 / Rsym value: 0.433 / % possible all: 82.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AHA Resolution: 1.67→65.09 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.948 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.101 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.417 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→65.09 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.673→1.717 Å / Total num. of bins used: 20
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