[English] 日本語
![](img/lk-miru.gif)
- PDB-7vb3: Crystal structure of hydroxynitrile lyase from Linum usitatissimum -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7vb3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of hydroxynitrile lyase from Linum usitatissimum | ||||||
![]() | Aliphatic (R)-hydroxynitrile lyase | ||||||
![]() | LYASE / hydroxynitrile lyase / NAD | ||||||
Function / homology | ![]() aliphatic (R)-hydroxynitrile lyase / aliphatic (R)-hydroxynitrile lyase activity / S-(hydroxymethyl)glutathione dehydrogenase [NAD(P)+] activity / formaldehyde catabolic process / alcohol dehydrogenase (NAD+) activity, zinc-dependent / zinc ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zheng, D. / Nakabayashi, M. / Asano, Y. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural characterization of Linum usitatissimum hydroxynitrile lyase: A new cyanohydrin decomposition mechanism involving a cyano-zinc complex. Authors: Zheng, D. / Nakabayashi, M. / Asano, Y. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 369 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 295 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 9.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 9 MB | Display | |
Data in XML | ![]() | 74.4 KB | Display | |
Data in CIF | ![]() | 112.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vb5C ![]() 7vb6C ![]() 1d1tS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 48167.195 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P93243, aliphatic (R)-hydroxynitrile lyase |
---|
-Non-polymers , 7 types, 1707 molecules ![](data/chem/img/NAD.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/BTB.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/BTB.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-MG / #6: Chemical | ChemComp-EDO / #7: Chemical | #8: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.51 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M BIS-TRIS, pH 6.5, 20% w/v polyethylene glycol mono methyl ether 5000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.48→167.866 Å / Num. obs: 269690 / % possible obs: 99.6 % / Redundancy: 6.1 % / Rpim(I) all: 0.04 / Rrim(I) all: 0.101 / Rsym value: 0.092 / Net I/av σ(I): 5.6 / Net I/σ(I): 10.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1D1T Resolution: 1.48→84.07 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.307 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.066 / 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: 73.01 Å2 / Biso mean: 17.294 Å2 / Biso min: 8.05 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.48→84.07 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.482→1.52 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|