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- PDB-4h8n: Crystal structure of conjugated polyketone reductase C2 from cand... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4h8n | ||||||
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Title | Crystal structure of conjugated polyketone reductase C2 from candida parapsilosis complexed with NADPH | ||||||
![]() | Conjugated polyketone reductase C2 | ||||||
![]() | OXIDOREDUCTASE / TIM BARREL / D-PANTOYL LACTONE | ||||||
Function / homology | ![]() 2-dehydropantolactone reductase / 2-dehydropantolactone reductase (A-specific) activity / oxidoreductase activity, acting on NAD(P)H as acceptor / cellular ketone metabolic process / aldo-keto reductase (NADPH) activity / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Qin, H.-M. / Yamamura, A. / Miyakawa, T. / Maruoka, S. / Ohtsuka, J. / Nagata, K. / Kataoka, M. / Shimizu, S. / Tanokura, M. | ||||||
![]() | ![]() Title: Structure of conjugated polyketone reductase from Candida parapsilosis IFO 0708 reveals conformational changes for substrate recognition upon NADPH binding Authors: Qin, H.-M. / Yamamura, A. / Miyakawa, T. / Kataoka, M. / Nagai, T. / Kitamura, N. / Urano, N. / Maruoka, S. / Ohtsuka, J. / Nagata, K. / Shimizu, S. / Tanokura, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 136.1 KB | Display | ![]() |
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PDB format | ![]() | 106.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3vxgC ![]() 3afy 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34976.574 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 2MM NADPH, 0.1M TRIS-HCL, 25% PEG 3350, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 24, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→20 Å / Num. obs: 46639 / % possible obs: 99.2 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 23.34 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3AFY ![]() 3afy Resolution: 1.8→19.51 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.935 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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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: 22.76 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.85 Å / Total num. of bins used: 20
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