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Yorodumi- PDB-2ris: Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ris | ||||||
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Title | Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase of candida albicans- alternate interpretation | ||||||
Components | 3,4-dihydroxy-2-butanone 4-phosphate synthase | ||||||
Keywords | ISOMERASE / alternate model / Magnesium / Manganese / Metal-binding / Riboflavin biosynthesis | ||||||
Function / homology | Function and homology information 3,4-dihydroxy-2-butanone-4-phosphate synthase / 3,4-dihydroxy-2-butanone-4-phosphate synthase activity / riboflavin biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Candida albicans (yeast) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.6 Å | ||||||
Authors | Stenkamp, R.E. / Le Trong, I. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2008 Title: Alternative models for two crystal structures of Candida albicans 3,4-dihydroxy-2-butanone 4-phosphate synthase. Authors: Le Trong, I. / Stenkamp, R.E. #1: Journal: J.Mol.Biol. / Year: 2004 Title: Potential anti-infective targets in pathogenic yeasts: structure and properties of 3,4-dihydroxy-2-butanone 4-phosphate synthase of Candida albicans. Authors: Echt, S. / Bauer, S. / Steinbacher, S. / Huber, R. / Bacher, A. / Fischer, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ris.cif.gz | 52.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ris.ent.gz | 38 KB | Display | PDB format |
PDBx/mmJSON format | 2ris.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ri/2ris ftp://data.pdbj.org/pub/pdb/validation_reports/ri/2ris | 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: 22684.982 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candida albicans (yeast) / Gene: RIB3 / Plasmid: pnco-carib3-syn / Production host: Escherichia coli (E. coli) / Strain (production host): xl1 / References: UniProt: Q5A3V6 |
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#2: 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: 2.21 Å3/Da / Density % sol: 44.34 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.542 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 3, 2003 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→51.5 Å / Num. obs: 24177 |
-Processing
Software |
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Refinement | Resolution: 1.6→51.5 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.926 / SU B: 1.575 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.103 / 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 mean: 11.594 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→51.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.642 Å / Total num. of bins used: 20
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