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Yorodumi- PDB-4mx5: Structure of ricin A chain bound with benzyl-(2-(2-amino-4-oxo-3,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mx5 | ||||||
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Title | Structure of ricin A chain bound with benzyl-(2-(2-amino-4-oxo-3,4-dihydropteridine-7-carboxamido)ethyl)carbamate | ||||||
Components | Ricin A chain | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / TOXIN / HYDROLASE / RIBOSOME-INACTIVATING PROTEIN / N-glycosidase / PTERIN / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å | ||||||
Authors | Jasheway, K.R. / Robertus, J.D. / Wiget, P.A. / Manzano, L.A. / Pruet, J.M. / Gao, G. / Saito, R. / Monzingo, A.F. / Anslyn, E.V. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2013 Title: Sulfur incorporation generally improves Ricin inhibition in pterin-appended glycine-phenylalanine dipeptide mimics. Authors: Wiget, P.A. / Manzano, L.A. / Pruet, J.M. / Gao, G. / Saito, R. / Monzingo, A.F. / Jasheway, K.R. / Robertus, J.D. / Anslyn, E.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mx5.cif.gz | 72.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mx5.ent.gz | 52.1 KB | Display | PDB format |
PDBx/mmJSON format | 4mx5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mx5_validation.pdf.gz | 728.8 KB | Display | wwPDB validaton report |
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Full document | 4mx5_full_validation.pdf.gz | 737 KB | Display | |
Data in XML | 4mx5_validation.xml.gz | 16 KB | Display | |
Data in CIF | 4mx5_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/4mx5 ftp://data.pdbj.org/pub/pdb/validation_reports/mx/4mx5 | HTTPS FTP |
-Related structure data
Related structure data | 4mx1C 1rtcS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 30067.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ricinus communis (castor bean) / Organ: seeds / Plasmid: PUTA / Production host: Escherichia coli (E. coli) / Strain (production host): JM101 / References: UniProt: P02879, rRNA N-glycosylase |
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#2: Chemical | ChemComp-5MX / |
#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: 2.7 Å3/Da / Density % sol: 54.41 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 1.3 M ammonium sulfate, 0.1 M sodium malonate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2011 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: single crystal, cylindrically bent, Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97648 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.52→50 Å / Num. obs: 52417 / % possible obs: 100 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.115 / Χ2: 1.277 / Net I/σ(I): 9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RTC Resolution: 1.52→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.27 / SU B: 1.419 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 92.93 Å2 / Biso mean: 24.534 Å2 / Biso min: 12.03 Å2
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Refinement step | Cycle: LAST / Resolution: 1.52→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.52→1.549 Å / Total num. of bins used: 20
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