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Yorodumi- PDB-4ijr: Crystal structure of Saccharomyces cerevisiae arabinose dehydroge... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ijr | ||||||
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Title | Crystal structure of Saccharomyces cerevisiae arabinose dehydrogenase Ara1 complexed with NADPH | ||||||
Components | D-arabinose dehydrogenase [NAD(P)+] heavy chain | ||||||
Keywords | OXIDOREDUCTASE / Tim Barrel / dehydrogenase / NADPH binding / cytosol | ||||||
Function / homology | Function and homology information D-arabinose 1-dehydrogenase [NAD(P)+] / D-arabinose 1-dehydrogenase (NAD+) activity / D-arabinose 1-dehydrogenase (NADP+) activity / Estrogen biosynthesis / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Pregnenolone biosynthesis / Fructose biosynthesis / Prednisone ADME / D-arabinose 1-dehydrogenase [NAD(P)+] activity ...D-arabinose 1-dehydrogenase [NAD(P)+] / D-arabinose 1-dehydrogenase (NAD+) activity / D-arabinose 1-dehydrogenase (NADP+) activity / Estrogen biosynthesis / Synthesis of bile acids and bile salts via 24-hydroxycholesterol / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Pregnenolone biosynthesis / Fructose biosynthesis / Prednisone ADME / D-arabinose 1-dehydrogenase [NAD(P)+] activity / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / RA biosynthesis pathway / aldose reductase (NADPH) activity / carbohydrate metabolic process / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Hu, X.Q. / Guo, P.C. / Li, W.F. / Zhou, C.Z. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2013 Title: Structures of Saccharomyces cerevisiaeD-arabinose dehydrogenase Ara1 and its complex with NADPH: implications for cofactor-assisted substrate recognition Authors: Hu, X.Q. / Guo, P.C. / Ma, J.D. / Li, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ijr.cif.gz | 284.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ijr.ent.gz | 232.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ijr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ijr_validation.pdf.gz | 950.5 KB | Display | wwPDB validaton report |
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Full document | 4ijr_full_validation.pdf.gz | 954.9 KB | Display | |
Data in XML | 4ijr_validation.xml.gz | 28.4 KB | Display | |
Data in CIF | 4ijr_validation.cif.gz | 40.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/4ijr ftp://data.pdbj.org/pub/pdb/validation_reports/ij/4ijr | HTTPS FTP |
-Related structure data
Related structure data | 4ijcSC 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: 38932.445 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: s288c / Gene: ARA1, YBR1127, YBR149W / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P38115, D-arabinose 1-dehydrogenase [NAD(P)+] #2: Chemical | #3: 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: 2.21 Å3/Da / Density % sol: 44.29 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 25% polyethylene glycol 3350, 0.1M Bis-Tris pH 6.5, 0.05M Cacl2, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.999 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 26, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 45854 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 21.98 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.178 / Mean I/σ(I) obs: 7.38 / Rsym value: 0.178 / % possible all: 95.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4IJC Resolution: 2→34.91 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / SU B: 10.639 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.184 / 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: 38.926 Å2
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Refinement step | Cycle: LAST / Resolution: 2→34.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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