+Open data
-Basic information
Entry | Database: PDB / ID: 3fwk | ||||||
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Title | Crystal Structure of Candida glabrata FMN Adenylyltransferase | ||||||
Components | FMN Adenylyltransferase | ||||||
Keywords | TRANSFERASE / FAD biosynthesis / alpha/beta protein / Rossmann-like fold / apo-form / extended loop region | ||||||
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 / SYNCHROTRON / Resolution: 1.2 Å | ||||||
Authors | Huerta, C. / Borek, D. / Zhang, H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structure and mechanism of a eukaryotic FMN adenylyltransferase. Authors: Huerta, C. / Borek, D. / Machius, M. / 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 | 3fwk.cif.gz | 131.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fwk.ent.gz | 103.1 KB | Display | PDB format |
PDBx/mmJSON format | 3fwk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fw/3fwk ftp://data.pdbj.org/pub/pdb/validation_reports/fw/3fwk | HTTPS FTP |
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-Related 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: 35985.723 Da / Num. of mol.: 1 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: Chemical | ChemComp-CL / |
#3: Sugar | ChemComp-BGC / |
#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: 2.01 Å3/Da / Density % sol: 38.78 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 6% (w/v) PEG 4000, 0.1 M Sodium acetate, pH 4.6,Temperature 289K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 16, 2006 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97924 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→50 Å / Num. all: 90728 / Num. obs: 90728 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Biso Wilson estimate: 14.6 Å2 / Rsym value: 0.07 / Net I/σ(I): 48.224 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 6 % / Mean I/σ(I) obs: 2.347 / Num. unique all: 4487 / Rsym value: 0.442 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Resolution: 1.2→50 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.97 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 1.103 / SU ML: 0.025 Isotropic thermal model: isotropic and anisotropic temperature factors Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.039 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 59.71 Å2 / Biso mean: 18.769 Å2 / Biso min: 9.89 Å2
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Refinement step | Cycle: LAST / Resolution: 1.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.199→1.23 Å / Total num. of bins used: 20
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