[English] 日本語
![](img/lk-miru.gif)
- PDB-3ek1: Crystal structure of aldehyde dehydrogenase from brucella meliten... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3ek1 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of aldehyde dehydrogenase from brucella melitensis biovar abortus 2308 | ||||||
![]() | Aldehyde dehydrogenase | ||||||
![]() | OXIDOREDUCTASE / SSGCID / ALDEHYDE DEHYDROGENASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | ![]() succinate-semialdehyde dehydrogenase [NAD(P)+] / succinate-semialdehyde dehydrogenase [NAD(P)+] activity / gamma-aminobutyric acid catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
![]() | ![]() Title: Crystal structure of aldehyde dehydrogenase from brucella melitensis biovar abortus 2308 Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 776.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 634.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 525.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 564.4 KB | Display | |
Data in XML | ![]() | 163.6 KB | Display | |
Data in CIF | ![]() | 240.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2opxS S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 53613.355 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: BIOVAR ABORTUS 2308 / Gene: gabD, BAB1_1655 / Plasmid: PET28-HISSMT / Production host: ![]() ![]() References: UniProt: Q2YRI3, succinate-semialdehyde dehydrogenase [NAD(P)+] #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-MES / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.58 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PROPLEX-96 F9: 1.0M AMMONIUM SULPHATE, 100MM MES PH 6.5, VAPOR DIFFUSION, TEMPERATURE 298K, pH 6.50, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 20, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 246609 / Num. obs: 231828 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.81 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 11.02 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 1.71 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2.3 / Num. unique all: 16866 / Rsym value: 0.354 / % possible all: 92.5 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() ![]() Starting model: pdb entry 2opx, modified Resolution: 2.1→19.78 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.67 / SU ML: 0.123 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.208 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 19.83 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→19.78 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.15 Å / Total num. of bins used: 20
|