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Yorodumi- PDB-4emr: Crystal Structure determination of type1 ribosome inactivating pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4emr | |||||||||
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Title | Crystal Structure determination of type1 ribosome inactivating protein complexed with 7-methylguanosine-triphosphate at 1.75A | |||||||||
Components | rRNA N-glycosidase | |||||||||
Keywords | HYDROLASE / 7-mgtp / RIP complex | |||||||||
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: 1.75 Å | |||||||||
Authors | Kumar, M. / Kushwaha, G.S. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P. | |||||||||
Citation | Journal: Proteins / Year: 2013 Title: First structural evidence of sequestration of mRNA cap structures by type 1 ribosome inactivating protein from Momordica balsamina. Authors: Kushwaha, G.S. / Yamini, S. / Kumar, M. / Sinha, M. / 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 | 4emr.cif.gz | 69.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4emr.ent.gz | 49.1 KB | Display | PDB format |
PDBx/mmJSON format | 4emr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4emr_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4emr_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4emr_validation.xml.gz | 15 KB | Display | |
Data in CIF | 4emr_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/4emr ftp://data.pdbj.org/pub/pdb/validation_reports/em/4emr | HTTPS FTP |
-Related structure data
Related structure data | 4emfC 4i47C 3mrwS 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: 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-MGP / |
#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: 2.42 Å3/Da / Density % sol: 49.17 % |
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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 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: Oct 21, 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: 1.75→35.03 Å / Num. obs: 24079 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 25.7 Å2 / Rsym value: 0.089 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.75→1.78 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.389 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3MRW Resolution: 1.75→35 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.527 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.14 / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 mean: 29.923 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.78 Å / Total num. of bins used: 20
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