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Yorodumi- PDB-6bdb: I-OnuI K227Y, D236A bound to A3G substrate (pre-cleavage complex) -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bdb | ||||||
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Title | I-OnuI K227Y, D236A bound to A3G substrate (pre-cleavage complex) | ||||||
Components |
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Keywords | HYDROLASE / Nucleic Acid | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Ophiostoma novo-ulmi subsp. americana (fungus) Ophiostoma novo-ulmi (Dutch elm disease fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å | ||||||
Authors | Brown, C. / Zhang, K. / McMurrough, T.A. / Laforet, M. / Gloor, G.B. / Edgell, D.R. / Junop, M. | ||||||
Citation | Journal: To Be Published Title: I-OnuI K227Y, D236A bound to A3G substrate (pre-cleavage complex) Authors: Laforet, M. / McMurrough, T.A. / Brown, C. / Junop, M. / Zhang, K. / Gloor, G.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bdb.cif.gz | 118.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bdb.ent.gz | 84.4 KB | Display | PDB format |
PDBx/mmJSON format | 6bdb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bdb_validation.pdf.gz | 438.5 KB | Display | wwPDB validaton report |
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Full document | 6bdb_full_validation.pdf.gz | 442 KB | Display | |
Data in XML | 6bdb_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | 6bdb_validation.cif.gz | 32.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/6bdb ftp://data.pdbj.org/pub/pdb/validation_reports/bd/6bdb | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35136.762 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ophiostoma novo-ulmi subsp. americana (fungus) Gene: HEG fusion, rps3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4VWW5 |
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#2: DNA chain | Mass: 7775.014 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Ophiostoma novo-ulmi (Dutch elm disease fungus) |
#3: DNA chain | Mass: 8198.330 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Ophiostoma novo-ulmi (Dutch elm disease fungus) |
#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: 49.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M DiAmmonium Phosphate 20% W/V PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9798 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9798 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→66.74 Å / Num. obs: 80496 / % possible obs: 100 % / Redundancy: 7.6 % / Rpim(I) all: 0.056 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 1.5→1.517 Å / Rpim(I) all: 0.327 |
-Processing
Software |
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Refinement | Resolution: 1.5→42.019 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.97 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→42.019 Å
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Refine LS restraints |
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LS refinement shell |
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