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Yorodumi- PDB-3bl5: Crystal structure of QueC from Bacillus subtilis: an enzyme invol... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bl5 | ||||||
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Title | Crystal structure of QueC from Bacillus subtilis: an enzyme involved in preQ1 biosynthesis | ||||||
Components | Queuosine biosynthesis protein queC | ||||||
Keywords | HYDROLASE / preQ1 biosynthesis / RNA modification / tRNA / Queuosine biosynthesis | ||||||
Function / homology | Function and homology information 7-cyano-7-deazaguanine synthase / ligase activity, forming carbon-nitrogen bonds / queuosine biosynthetic process / zinc ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Cicmil, N. / Huang, R.H. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Crystal structure of QueC from Bacillus subtilis: An enzyme involved in preQ(1) biosynthesis. Authors: Cicmil, N. / Huang, R.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bl5.cif.gz | 233 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bl5.ent.gz | 189.8 KB | Display | PDB format |
PDBx/mmJSON format | 3bl5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bl5_validation.pdf.gz | 495.4 KB | Display | wwPDB validaton report |
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Full document | 3bl5_full_validation.pdf.gz | 557.7 KB | Display | |
Data in XML | 3bl5_validation.xml.gz | 49.7 KB | Display | |
Data in CIF | 3bl5_validation.cif.gz | 65.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/3bl5 ftp://data.pdbj.org/pub/pdb/validation_reports/bl/3bl5 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 24557.139 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: queC, ykvJ / Plasmid: PLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O31675, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-PO4 / #5: Water | ChemComp-HOH / | |
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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: 2.88 Å3/Da / Density % sol: 57.29 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25% PEG 6000, 100 mM NaCl, 100 mM MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→50 Å / Num. obs: 35642 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→50 Å / σ(F): 2 / σ(I): 2
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Refinement step | Cycle: LAST / Resolution: 2.95→50 Å
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