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- PDB-4ijc: Crystal structure of arabinose dehydrogenase Ara1 from Saccharomy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ijc | ||||||
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Title | Crystal structure of arabinose dehydrogenase Ara1 from Saccharomyces cerevisiae | ||||||
![]() | D-arabinose dehydrogenase [NAD(P)+] heavy chain | ||||||
![]() | OXIDOREDUCTASE / BETA BARREL / TIM barrel | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hu, X.Q. / Guo, P.C. / Li, W.F. / Zhou, C.Z. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 274.6 KB | Display | ![]() |
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PDB format | ![]() | 224.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461.5 KB | Display | ![]() |
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Full document | ![]() | 467 KB | Display | |
Data in XML | ![]() | 28.1 KB | Display | |
Data in CIF | ![]() | 40.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ijrC ![]() 1zuaS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Strain: s288c / Gene: ARA1, YBR1127, YBR149W / Plasmid: pET28 / Production host: ![]() ![]() References: UniProt: P38115, D-arabinose 1-dehydrogenase [NAD(P)+] #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.18 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25% polyethylene glycol 3350, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 18, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.919 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 41412 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 19.557 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 10 / Rsym value: 0.257 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ZUA Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.919 / SU B: 11.81 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.214 / 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: 33.911 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.102→2.157 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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