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Yorodumi- PDB-4kkv: Crystal structure of candida glabrata FMN adenylyltransferase D18... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kkv | ||||||
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Title | Crystal structure of candida glabrata FMN adenylyltransferase D181A Mutant | ||||||
Components | Similar to uniprot|P38913 Saccharomyces cerevisiae YDL045c FAD synthetase | ||||||
Keywords | TRANSFERASE / alpha/beta protein / Rossmann-like fold / FAD biosynthesis | ||||||
Function / homology | Function and homology information FAD synthase / FMN adenylyltransferase activity / FAD biosynthetic process / magnesium ion binding / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Candida glabrata (fungus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||
Authors | Huerta, C. / Zhang, H. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: The "Super Mutant" of Yeast FMN Adenylyltransferase Enhances the Enzyme Turnover Rate by Attenuating Product Inhibition. Authors: Huerta, C. / Grishin, N.V. / Zhang, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kkv.cif.gz | 85.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kkv.ent.gz | 63.6 KB | Display | PDB format |
PDBx/mmJSON format | 4kkv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kkv_validation.pdf.gz | 443.3 KB | Display | wwPDB validaton report |
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Full document | 4kkv_full_validation.pdf.gz | 445.9 KB | Display | |
Data in XML | 4kkv_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 4kkv_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/4kkv ftp://data.pdbj.org/pub/pdb/validation_reports/kk/4kkv | HTTPS FTP |
-Related structure data
Related structure data | 3fwkS S: Starting model for refinement |
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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: 35941.715 Da / Num. of mol.: 1 / Mutation: D181A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida glabrata (fungus) / Strain: NCYC / Gene: CAGL0K01397g, FAD1 / Plasmid: pHIS parallel / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6FNA9, FAD synthase |
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#2: Sugar | ChemComp-BGC / |
#3: Chemical | ChemComp-CL / |
#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: 2.02 Å3/Da / Density % sol: 39.17 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.1 M Sodium acetate, pH 5.0, 8% w/v PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 15, 2010 / Details: Mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→50 Å / Num. all: 30336 / Num. obs: 30119 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 5.5 % / Biso Wilson estimate: 17.85 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 1.74→1.77 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.497 / Mean I/σ(I) obs: 1.26 / Num. unique all: 1410 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 3FWK Resolution: 1.74→24.4 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.346 / SU ML: 0.077 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.121 Å2
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Refinement step | Cycle: LAST / Resolution: 1.74→24.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.74→1.785 Å / Total num. of bins used: 20
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