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Yorodumi- PDB-4fgc: Crystal Structure of Active Site Mutant C55A of Nitrile Reductase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fgc | ||||||
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Title | Crystal Structure of Active Site Mutant C55A of Nitrile Reductase QueF, Bound to Substrate PreQ0 | ||||||
Components | NADPH-dependent 7-cyano-7-deazaguanine reductase | ||||||
Keywords | OXIDOREDUCTASE / beta barrel / pterin binding fold / tunnel fold / tRNA modification enzyme / 7-cyano-7-deazaguanine (PreQ0) binding / NADPH binding | ||||||
Function / homology | Function and homology information preQ1 synthase / preQ1 synthase activity / queuosine biosynthetic process / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis subsp. subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.498 Å | ||||||
Authors | Stec, B. / Swairjo, M.A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structural basis of biological nitrile reduction. Authors: Chikwana, V.M. / Stec, B. / Lee, B.W. / de Crecy-Lagard, V. / Iwata-Reuyl, D. / Swairjo, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fgc.cif.gz | 167.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fgc.ent.gz | 132.3 KB | Display | PDB format |
PDBx/mmJSON format | 4fgc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fgc_validation.pdf.gz | 737.6 KB | Display | wwPDB validaton report |
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Full document | 4fgc_full_validation.pdf.gz | 763.4 KB | Display | |
Data in XML | 4fgc_validation.xml.gz | 33.9 KB | Display | |
Data in CIF | 4fgc_validation.cif.gz | 45.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/4fgc ftp://data.pdbj.org/pub/pdb/validation_reports/fg/4fgc | HTTPS FTP |
-Related structure data
Related structure data | 4f8bSC 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
#1: Protein | Mass: 19364.891 Da / Num. of mol.: 5 / Mutation: C55A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria) Strain: 168 / Gene: BSU13750, queF, ykvM / Plasmid: pET-30Xa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O31678, preQ1 synthase #2: Chemical | ChemComp-PQ0 / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-PE4 / | #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: 2.5 Å3/Da / Density % sol: 50.79 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion / pH: 7.4 Details: 16-20% PEG500 MME, 60 mM imidazole, 40 mM imidazolium chloride, pH 7.4, 30 mM calcium chloride, VAPOR DIFFUSION, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.000003 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 11, 2011 / Details: mirrors |
Radiation | Monochromator: Side-scattering cuberoot I-beam bent single crystal, asymmetric cut 12.2 degrees Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000003 Å / Relative weight: 1 |
Reflection | Resolution: 2.498→22.151 Å / Num. all: 34498 / Num. obs: 31577 / % possible obs: 91.6 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 46.6 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.498→2.54 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1498 / % possible all: 88.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 4F8B Resolution: 2.498→22.15 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.86 / SU B: 14.033 / SU ML: 0.304 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.711 / ESU R Free: 0.368 / 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 mean: 39.309 Å2
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Refinement step | Cycle: LAST / Resolution: 2.498→22.15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.498→2.562 Å / Total num. of bins used: 20
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