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Yorodumi- PDB-4imv: Ricin A-chain variant 1-33/44-198 with engineered disulfide bond,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4imv | ||||||
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Title | Ricin A-chain variant 1-33/44-198 with engineered disulfide bond, R48C/T77C/D75N | ||||||
Components | Ricin | ||||||
Keywords | HYDROLASE / Ricin / immunogen / vaccine / thermal stable / Ribosome Inactivating Protein (RIP) | ||||||
Function / homology | Function and homology information rRNA N-glycosylase / rRNA N-glycosylase activity / AMP binding / defense response / toxin activity / carbohydrate binding / killing of cells of another organism / negative regulation of translation Similarity search - Function | ||||||
Biological species | Ricinus communis (castor bean) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Legler, P.M. / Compton, J.R. / Millard, C.B. | ||||||
Citation | Journal: Toxins (Basel) / Year: 2013 Title: Disruption of the Putative Vascular Leak Peptide Sequence in the Stabilized Ricin Vaccine Candidate RTA1-33/44-198. Authors: Janosi, L. / Compton, J.R. / Legler, P.M. / Steele, K.E. / Davis, J.M. / Matyas, G.R. / Millard, C.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4imv.cif.gz | 43.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4imv.ent.gz | 33.3 KB | Display | PDB format |
PDBx/mmJSON format | 4imv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/im/4imv ftp://data.pdbj.org/pub/pdb/validation_reports/im/4imv | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 21414.203 Da / Num. of mol.: 1 / Fragment: unp residues 36-233 / Mutation: R48C, T77C, D75N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ricinus communis (castor bean) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02879, rRNA N-glycosylase |
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#2: Chemical | ChemComp-SO4 / |
#3: 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: 2.06 Å3/Da / Density % sol: 40.37 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: 0.17 M Ammonium Sulfate, 25.5% (w/v) Peg 4000, 15% Glycerol , pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 150 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Jun 18, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→57.48 Å / Num. all: 8721 / Num. obs: 8640 / % possible obs: 99.1 % / Observed criterion σ(I): 3 / Redundancy: 6.88 % / Biso Wilson estimate: 20.2 Å2 / Rsym value: 0.1191 / Net I/σ(I): 13.01 |
Reflection shell | Resolution: 2.25→2.34 Å / Redundancy: 4.18 % / Mean I/σ(I) obs: 3.62 / Num. unique all: 939 / Rsym value: 0.4191 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→57.48 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.902 / Cross valid method: THROUGHOUT / σ(I): 3 / ESU R: 0.359 / ESU R Free: 0.229 / 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 mean: 23.598 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→57.48 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.308 Å / Total num. of bins used: 20
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