[English] 日本語
![](img/lk-miru.gif)
- PDB-4k3i: Crystal Structure of the Quinol Form of Methylamine Dehydrogenase... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4k3i | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Quinol Form of Methylamine Dehydrogenase in Complex with the Diferrous Form of MauG, C2 Space Group | ||||||
![]() |
| ||||||
![]() | OXIDOREDUCTASE | ||||||
Function / homology | ![]() methylamine dehydrogenase (amicyanin) / methylamine dehydrogenase (amicyanin) activity / methylamine metabolic process / amine dehydrogenase activity / amine metabolic process / Oxidoreductases / cytochrome-c peroxidase activity / outer membrane-bounded periplasmic space / periplasmic space / electron transfer activity ...methylamine dehydrogenase (amicyanin) / methylamine dehydrogenase (amicyanin) activity / methylamine metabolic process / amine dehydrogenase activity / amine metabolic process / Oxidoreductases / cytochrome-c peroxidase activity / outer membrane-bounded periplasmic space / periplasmic space / electron transfer activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Yukl, E.Y. / Wilmot, C.M. | ||||||
![]() | ![]() Title: Structures of MauG in complex with quinol and quinone MADH. Authors: Yukl, E.T. / Jensen, L.M. / Davidson, V.L. / Wilmot, C.M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 695.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 572.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 81 KB | Display | |
Data in CIF | ![]() | 121.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3sxtS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
-Protein / Antibody / Methylamine dehydrogenase ... , 3 types, 6 molecules ABCEDF
#1: Protein | Mass: 41146.629 Da / Num. of mol.: 2 / Fragment: UNP residues 21-387 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 15041.593 Da / Num. of mol.: 2 / Fragment: UNP residues 58-188 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P22619, methylamine dehydrogenase (amicyanin) #3: Protein | Mass: 42321.152 Da / Num. of mol.: 2 / Fragment: UNP residues 33-417 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|
-Non-polymers , 6 types, 1722 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEC.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-HEC / #6: Chemical | ChemComp-NA / #7: Chemical | ChemComp-EDO / #8: Chemical | ChemComp-ACT / | #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.31 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: Drops contained 1uL protein with 3uL reservoir solution. WT-MauG and MADH were each reduced in an anaerobic glove box prior to preparing the protein mixture for crystallization. Protein ...Details: Drops contained 1uL protein with 3uL reservoir solution. WT-MauG and MADH were each reduced in an anaerobic glove box prior to preparing the protein mixture for crystallization. Protein mixture: 100uM reduced WT-MauG and 50uM reduced MADH in 10mM potassium phosphate pH7.5 with 2mM sodium dithionite. Reservoir solution contained: 24% w/v PEG 8000, 0.1M sodium acetate, 0.1M MES pH 6.4 and 2mM sodium dithionite. Crystallization was carried out in an anaerobic glove box at ambient temperature., VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 5, 2010 / Details: BIOMORPH MIRRORS (KIRKPATRICK- BAEZ CONFIGURATION) |
Radiation | Monochromator: SI(111) DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 132241 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rsym value: 0.104 / Net I/σ(I): 13.55 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.65 / Rsym value: 0.551 / % possible all: 99.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 3SXT Resolution: 2→43.06 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.983 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.748 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→43.06 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.053 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|