[English] 日本語
![](img/lk-miru.gif)
- PDB-2ziz: Crystal structure of Mycobacterium tuberculosis S-adenosyl-L-homo... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 2ziz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with NAD and 3-deazaadenosine | ||||||
![]() | Adenosylhomocysteinase | ||||||
![]() | HYDROLASE / Protein-substrate complex / dimer of dimers / NAD binding domain / 37 amino acid insertional region / One-carbon metabolism | ||||||
Function / homology | ![]() adenosylhomocysteinase / methionine catabolic process / adhesion of symbiont to host cell / adenosine metabolic process / adenosylhomocysteinase / adenosylhomocysteinase activity / entry of bacterium into host cell / S-adenosylmethionine cycle / zymogen binding / NAD+ binding ...adenosylhomocysteinase / methionine catabolic process / adhesion of symbiont to host cell / adenosine metabolic process / adenosylhomocysteinase / adenosylhomocysteinase activity / entry of bacterium into host cell / S-adenosylmethionine cycle / zymogen binding / NAD+ binding / peptidoglycan-based cell wall / one-carbon metabolic process / extracellular region / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Reddy, M.C.M. / Gokulan, K. / Shetty, N.D. / Owen, J.L. / Ioerger, T.R. / Sacchettini, J.C. | ||||||
![]() | ![]() Title: Crystal structures of Mycobacterium tuberculosis S-adenosyl-L-homocysteine hydrolase in ternary complex with substrate and inhibitors. Authors: Reddy, M.C. / Kuppan, G. / Shetty, N.D. / Owen, J.L. / Ioerger, T.R. / Sacchettini, J.C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 397.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 325.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.6 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 83.2 KB | Display | |
Data in CIF | ![]() | 113.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2zj0C ![]() 2zj1C ![]() 3ce6SC ![]() 3dhyC C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 54387.410 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P60176, UniProt: P9WGV3*PLUS, adenosylhomocysteinase #2: Chemical | ChemComp-AD3 / #3: Chemical | ChemComp-NAD / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.16 % |
---|---|
Crystal grow | Temperature: 291.5 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% PEG 1000, 200 mM Imidazole pH 8.0, 100 mM Calcium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 291.5K |
-Data collection
Diffraction | Mean temperature: 120 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2005 / Details: Mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.964 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→100 Å / Num. obs: 93598 / % possible obs: 94.4 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 42.15 Å2 |
Reflection shell | Resolution: 2.2→2.26 Å / % possible all: 70.71 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 3CE6 Resolution: 2.2→38.18 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.895 / SU B: 7.397 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.332 / ESU R Free: 0.269 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.792 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→38.18 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.26 Å / Total num. of bins used: 20
|