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Yorodumi- PDB-6ury: Crystal structure of ricin A chain in complex with inhibitor 9-ox... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ury | ||||||
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Title | Crystal structure of ricin A chain in complex with inhibitor 9-oxo-4-fluorenecarboxamide | ||||||
Components | Ricin | ||||||
Keywords | Hydrolase/Hydrolase Inhibitor / Ricin A chain / RTA / Hydrolase / Toxin / Inhibitor / 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: 1.54 Å | ||||||
Authors | Harijan, R.K. / Li, X.P. / Bonanno, J.B. / Almo, S.C. / Tumer, N.E. / Schramm, V.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Infect Dis. / Year: 2020 Title: Small Molecule Inhibitors Targeting the Interaction of Ricin Toxin A Subunit with Ribosomes. Authors: Li, X.P. / Harijan, R.K. / Kahn, J.N. / Schramm, V.L. / Tumer, N.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ury.cif.gz | 141 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ury.ent.gz | 106.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ury.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ury_validation.pdf.gz | 353 KB | Display | wwPDB validaton report |
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Full document | 6ury_full_validation.pdf.gz | 354.3 KB | Display | |
Data in XML | 6ury_validation.xml.gz | 2.5 KB | Display | |
Data in CIF | 6ury_validation.cif.gz | 12.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ur/6ury ftp://data.pdbj.org/pub/pdb/validation_reports/ur/6ury | HTTPS FTP |
-Related structure data
Related structure data | 6urwC 6urxC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 3 - 261 / Label seq-ID: 4 - 262
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-Components
#1: Protein | Mass: 30067.953 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ricinus communis (castor bean) / Production host: Escherichia coli (E. coli) / References: UniProt: P02879, rRNA N-glycosylase #2: Chemical | ChemComp-R6T / | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49.01 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 100 mM Tris pH 7.0, 200 mM Magnesium Chloride, 2.5 M Sodium Chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jun 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→66.14 Å / Num. obs: 88500 / % possible obs: 100 % / Redundancy: 25.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.03 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.54→1.57 Å / Redundancy: 11 % / Rmerge(I) obs: 1.2 / Mean I/σ(I) obs: 2 / Num. unique obs: 4211 / CC1/2: 0.75 / Rpim(I) all: 0.36 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RTC Resolution: 1.54→66.14 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.394 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.075 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61.69 Å2 / Biso mean: 17.912 Å2 / Biso min: 7.79 Å2
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Refinement step | Cycle: final / Resolution: 1.54→66.14 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 16992 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.54→1.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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