[English] 日本語
![](img/lk-miru.gif)
- PDB-8b5t: Crystal structure of Quinonoid dihydropteridine reductase from Le... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8b5t | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Quinonoid dihydropteridine reductase from Leishmania major | ||||||
![]() | Quinonoid dihydropteridine reductase | ||||||
![]() | OXIDOREDUCTASE / QDPR / LEISHMANIA | ||||||
Function / homology | ![]() 1.6.99.7 / 6,7-dihydropteridine reductase / 6,7-dihydropteridine reductase activity / NADH binding / tetrahydrobiopterin biosynthetic process / L-phenylalanine catabolic process / NADPH binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Robinson, D.A. / Fairlamb, A.H. | ||||||
Funding support | 1items
| ||||||
![]() | ![]() Title: Crystal structure of Quinonoid dihydropteridine reductase from Leishmania major Authors: Robinson, D.A. / Fairlamb, A.H. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 139.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 108 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 438.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 444.9 KB | Display | |
Data in XML | ![]() | 28.5 KB | Display | |
Data in CIF | ![]() | 41.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1dirS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Protein | Mass: 23707.775 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: QDPR-7, QDPR, QDPR-2, QDPR-3, QDPR-4, QDPR-5, QDPR-6, LMJF_34_4360, LMJF_34_4390, LMJF_34_4420, LMJF_34_4450, LMJF_34_4480, LMJF_34_4510 Production host: ![]() ![]() References: UniProt: Q4Q290, 6,7-dihydropteridine reductase, 1.6.99.7 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.58 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5.5 / Details: 15% PEG4000, 0.2M MgCl2, 0.1M Na ACETATE pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92045 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→39.5 Å / Num. obs: 39899 / % possible obs: 99.2 % / Redundancy: 8.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.072 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.781 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 3192 / CC1/2: 0.8 / % possible all: 98.1 |
-Phasing
Phasing | Method: ![]() |
---|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1DIR Resolution: 2.1→39.5 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.131 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.216 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 155.29 Å2 / Biso mean: 36.974 Å2 / Biso min: 14.11 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→39.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|