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Yorodumi- PDB-3rl9: Crystal Structure of the complex of type I RIP with the hydrolyze... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rl9 | ||||||
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Title | Crystal Structure of the complex of type I RIP with the hydrolyzed product of dATP, adenine at 1.9 A resolution | ||||||
Components | Ribosome inactivating proteinRibosome-inactivating protein | ||||||
Keywords | HYDROLASE / RIP / RNA N-glycosidase / Plant protein / 6-aminopurine / inactivation | ||||||
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: 1.9 Å | ||||||
Authors | Kushwaha, G.S. / Pandey, N. / 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 | 3rl9.cif.gz | 65.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rl9.ent.gz | 47 KB | Display | PDB format |
PDBx/mmJSON format | 3rl9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rl/3rl9 ftp://data.pdbj.org/pub/pdb/validation_reports/rl/3rl9 | HTTPS FTP |
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-Related structure data
Related structure data | 3n1nC 3s9qC 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 / 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 | ChemComp-GOL / |
#4: Chemical | ChemComp-ADE / |
#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: 2.38 Å3/Da / Density % sol: 48.29 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 14% PEG 6000, 0.1M Sodium Phosphate , pH 6.7 , VAPOR DIFFUSION, HANGING DROP, temperature 298 K |
-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: May 13, 2010 / Details: mirror |
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: 1.9→65 Å / Num. all: 18659 / Num. obs: 18659 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.8 Å2 / Rsym value: 0.101 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.9→1.95 Å / Mean I/σ(I) obs: 4.1 / Rsym value: 0.628 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AHA Resolution: 1.9→29 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.271 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.156 / 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: 30.719 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→29 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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