[English] 日本語
![](img/lk-miru.gif)
- PDB-7qzl: Amine Dehydrogenase from Cystobacter fuscus (CfusAmDH) W145A muta... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7qzl | ||||||
---|---|---|---|---|---|---|---|
Title | Amine Dehydrogenase from Cystobacter fuscus (CfusAmDH) W145A mutant with NADP+ and pentylamine | ||||||
![]() | Amine Dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / Amine Dehydrogenase / NADP | ||||||
Function / homology | 2,4-diaminopentanoate dehydrogenase, C-terminal domain / 2,4-diaminopentanoate dehydrogenase C-terminal domain / NAD(P)-binding domain superfamily / nucleotide binding / AMYLAMINE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2,4-diaminopentanoate dehydrogenase C-terminal domain-containing protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bennett, M. / Ducrot, L. / Vaxelaire-Vergne, C. / Grogan, G. | ||||||
Funding support | 1items
| ||||||
![]() | ![]() Title: Cover Feature: Expanding the Substrate Scope of Native Amine Dehydrogenases through In Silico Structural Exploration and Targeted Protein Engineering (ChemCatChem 22/2022) Authors: Ducrot, L. / Bennett, M. / Andre-Leroux, G. / Elisee, E. / Marynberg, S. / Fossey-Jouenne, A. / Zaparucha, A. / Grogan, G. / Vergne-Vaxelaire, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 157.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 121.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7qznC ![]() 6iauS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Components on special symmetry positions |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 2 - 342 / Label seq-ID: 6 - 346
|
-
Components
#1: Protein | Mass: 37291.008 Da / Num. of mol.: 2 / Mutation: W145A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 45.96 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.1 M bis-Tris pH 5.5; 25% PEG 3350 10 mM NADP, 10 mM n-pentylamine |
-Data collection
Diffraction | Mean temperature: 120 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 25, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976284 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→47.4 Å / Num. obs: 109306 / % possible obs: 100 % / Redundancy: 12.2 % / Biso Wilson estimate: 17 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.04 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.5→1.53 Å / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 5350 / CC1/2: 0.9 / Rpim(I) all: 0.4 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6IAU Resolution: 1.5→47.4 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.293 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.068 / 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: 79.33 Å2 / Biso mean: 20.362 Å2 / Biso min: 11.55 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→47.4 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Ens-ID: 1 / Number: 10644 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|