[English] 日本語
![](img/lk-miru.gif)
- PDB-6aym: Crystal structure of Campylobacter jejuni 5'-methylthioadenosine/... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6aym | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Campylobacter jejuni 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) | ||||||
![]() | 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() aminodeoxyfutalosine nucleosidase / 6-amino-6-deoxyfutalosine hydrolase activity / ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Harijan, R.K. / Ducati, R.G. / Bonanno, J.B. / Almo, S.C. / Schramm, V.L. | ||||||
![]() | ![]() Title: Transition-State Analogues of Campylobacter jejuni 5'-Methylthioadenosine Nucleosidase. Authors: Ducati, R.G. / Harijan, R.K. / Cameron, S.A. / Tyler, P.C. / Evans, G.B. / Schramm, V.L. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 117.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 88.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6ayoC ![]() 6ayqC ![]() 6ayrC ![]() 6aysC ![]() 6aytC ![]() 4wknS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 0 / Auth seq-ID: 0 - 228 / Label seq-ID: 10 - 238
|
-
Components
#1: Protein | Mass: 26312.426 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: A0A1E7P7U4, UniProt: Q0PC20*PLUS, ![]() #2: Chemical | ChemComp-EDO / ![]() #3: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 47.2 % |
---|---|
Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 100 mM MES pH 6.5, 600 mM Sodium Chloride, 20% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 14, 2017 |
Radiation | Monochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.25→70.05 Å / Num. obs: 134158 / % possible obs: 98.3 % / Redundancy: 7.3 % / CC1/2: 0.99 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.25→1.27 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 6445 / CC1/2: 0.65 / % possible all: 96.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 4WKN Resolution: 1.25→70.05 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / SU B: 0.884 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.048 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.327 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.25→70.05 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|