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Yorodumi- PDB-3n1n: Crystal structure of the complex of type I ribosome inactivating ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3n1n | |||||||||
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Title | Crystal structure of the complex of type I ribosome inactivating protein with guanine at 2.2A resolution | |||||||||
Components | Ribosome inactivating proteinRibosome-inactivating protein | |||||||||
Keywords | HYDROLASE / RIP | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.23 Å | |||||||||
Authors | Kushwaha, G.S. / Singh, N. / Sinha, M. / Kaur, P. / Betzel, C. / 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 | 3n1n.cif.gz | 68.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3n1n.ent.gz | 48.9 KB | Display | PDB format |
PDBx/mmJSON format | 3n1n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n1/3n1n ftp://data.pdbj.org/pub/pdb/validation_reports/n1/3n1n | HTTPS FTP |
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-Related structure data
Related structure data | 3rl9C 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*PLUS, rRNA N-glycosylase |
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#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-GUN / |
#4: Water | ChemComp-HOH / |
Sequence details | THE SEQUENCE GIVEN FOR MOMORDICA BALSAMINA IS CORRECT, ITS GENBANK ACCESSION NO. IS HM367595. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.55 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Phosphate buffer, PEG6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 292 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 22, 2009 / Details: Mirror |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.23→20 Å / Num. all: 12690 / Num. obs: 12622 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 45 Å2 |
Reflection shell | Resolution: 2.23→2.25 Å / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AHA Resolution: 2.23→19.95 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 112384.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.9085 Å2 / ksol: 0.272043 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.23→19.95 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.23→2.37 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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