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- PDB-7vb6: Crystal structure of hydroxynitrile lyase from Linum usitatissium... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7vb6 | ||||||
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Title | Crystal structure of hydroxynitrile lyase from Linum usitatissium complexed with (R)-2-hydroxy-2-methylbutanenitrile | ||||||
![]() | Aliphatic (R)-hydroxynitrile lyase | ||||||
![]() | LYASE / Hydroxynitrile lyase / ZN / 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 | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 362.6 KB | Display | ![]() |
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PDB format | ![]() | 290 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 7 MB | Display | ![]() |
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Full document | ![]() | 7 MB | Display | |
Data in XML | ![]() | 72.6 KB | Display | |
Data in CIF | ![]() | 108.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vb3SC ![]() 7vb5C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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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 |
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-Non-polymers , 8 types, 1458 molecules ![](data/chem/img/NAD.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/5Z9.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/BTB.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/5Z9.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/BTB.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-MG / #5: Chemical | ChemComp-5Z9 / ( #6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-GOL / #8: Chemical | ChemComp-BTB / #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.93 % |
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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 monomethyl ether 5000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Feb 13, 2020 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.723→169.255 Å / Num. all: 168508 / Num. obs: 168508 / % possible obs: 97 % / Redundancy: 6.2 % / Rpim(I) all: 0.049 / Rrim(I) all: 0.123 / Rsym value: 0.113 / Net I/av σ(I): 5.2 / Net I/σ(I): 9.9 / Num. measured all: 1048056 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7VB3 Resolution: 1.74→49.85 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.5 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.109 / 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: 87.92 Å2 / Biso mean: 22.148 Å2 / Biso min: 8.49 Å2
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Refinement step | Cycle: final / Resolution: 1.74→49.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.74→1.78 Å / Rfactor Rfree error: 0
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