[English] 日本語
![](img/lk-miru.gif)
- PDB-2r6x: Structure of a D35N variant PduO-type ATP:co(I)rrinoid adenosyltr... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2r6x | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of a D35N variant PduO-type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri complexed with ATP | ||||||
![]() | Cobalamin adenosyltransferase PduO-like protein | ||||||
![]() | TRANSFERASE / adenosyltransferase variant / ATP binding | ||||||
Function / homology | ![]() corrinoid adenosyltransferase / corrinoid adenosyltransferase activity / cobalamin biosynthetic process / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | St Maurice, M. / Mera, P.E. / Escalante-Semerena, J.C. / Rayment, I. | ||||||
![]() | ![]() Title: Structural and functional analyses of the human-type corrinoid adenosyltransferase (PduO) from Lactobacillus reuteri. Authors: Mera, P.E. / St Maurice, M. / Rayment, I. / Escalante-Semerena, J.C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 87.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 65.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 16.5 KB | Display | |
Data in CIF | ![]() | 22.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||
2 | ![]()
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
| ||||||||||||
Details | The biological unit is a trimer. There are two monomers in the asymmetric unit. Each monomer forms its own biological unit. The biological units are generated from the operations: -x+y, -x, z and -y, x-y, z. |
-
Components
#1: Protein | Mass: 22381.332 Da / Num. of mol.: 2 / Mutation: D35N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-MG / #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.34 % |
---|---|
Crystal grow | Temperature: 300 K / Method: vapor diffusion / pH: 6 Details: ANOXIC, 16% PEG 8000, 0.1 M MES, 200 mM KCl, 30 ug/mL FMN reductase, 50 mM NADH, 10 mM FMN, 10 mM hydroxycobalamin, 10 mM MgCl2, 10 mM ATP, pH 6.0, vapor diffusion, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: May 25, 2007 / Details: Montel |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.61→30 Å / Num. obs: 12422 / % possible obs: 99.6 % / Redundancy: 7.5 % / Biso Wilson estimate: 29.4 Å2 / Rsym value: 6.8 / Net I/σ(I): 26.1 |
Reflection shell | Resolution: 2.61→2.66 Å / Redundancy: 4.9 % / Rsym value: 0.177 / % possible all: 99.5 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.61→30 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.862 / SU B: 10.706 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 30.817 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.61→30 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.61→2.663 Å / Total num. of bins used: 20
|