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- PDB-8b5u: Crystal structure of Quinonoid dihydropteridine reductase from Le... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8b5u | ||||||
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Title | Crystal structure of Quinonoid dihydropteridine reductase from Leishmania donovani | ||||||
![]() | Quinonoid dihydropteridine reductase | ||||||
![]() | OXIDOREDUCTASE / QDPR / LEISHMANIA | ||||||
Function / homology | 6,7-dihydropteridine reductase / 6,7-dihydropteridine reductase activity / short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / Quinonoid dihydropteridine reductase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Robinson, D.A. / Fairlamb, A.H. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal structure of Quinonoid dihydropteridine reductase from Leishmania donovani Authors: Robinson, D.A. / Fairlamb, A.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 60.1 KB | Display | ![]() |
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PDB format | ![]() | 41.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.9 KB | Display | ![]() |
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Full document | ![]() | 426.8 KB | Display | |
Data in XML | ![]() | 11.7 KB | Display | |
Data in CIF | ![]() | 16.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1dirS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 25852.143 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: CGC21_27355, LdCL_340051200, LdCL_340051500, LDHU3_34.6510 Production host: ![]() ![]() References: UniProt: A0A3S5H7Y1, 6,7-dihydropteridine reductase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.02 Å3/Da / Density % sol: 59.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 13-18% PEG 8000, 20% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 13, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97625 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.8→48.58 Å / Num. obs: 29308 / % possible obs: 100 % / Redundancy: 18.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.017 / Rrim(I) all: 0.071 / Net I/σ(I): 21.6 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DIR Resolution: 1.8→47.1 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.485 / SU ML: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.1 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 113.28 Å2 / Biso mean: 41.637 Å2 / Biso min: 24.89 Å2
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Refinement step | Cycle: final / Resolution: 1.8→47.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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