[English] 日本語
Yorodumi- PDB-5b7q: Structures and functional analysis of periplasmic 5-methylthioade... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b7q | ||||||
---|---|---|---|---|---|---|---|
Title | Structures and functional analysis of periplasmic 5-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Aeromonas hydrophila | ||||||
Components | MTA/SAH nucleosidase | ||||||
Keywords | HYDROLASE / Aeromonas hydrophila / MtaN-1 / MtaN-2 / SAH / MTA / 5-DAO | ||||||
Function / homology | Function and homology information methylthioadenosine nucleosidase / adenosylhomocysteine nucleosidase / adenosylhomocysteine nucleosidase activity / methylthioadenosine nucleosidase activity / nucleoside metabolic process Similarity search - Function | ||||||
Biological species | Aeromonas hydrophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.493 Å | ||||||
Authors | Xu, Y. | ||||||
Citation | Journal: Biochemistry / Year: 2017 Title: Structural and Functional Analyses of Periplasmic 5'-Methylthioadenosine/S-Adenosylhomocysteine Nucleosidase from Aeromonas hydrophila. Authors: Xu, Y. / Wang, L. / Chen, J. / Zhao, J. / Fan, S. / Dong, Y. / Ha, N.C. / Quan, C. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5b7q.cif.gz | 205.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5b7q.ent.gz | 165.7 KB | Display | PDB format |
PDBx/mmJSON format | 5b7q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/5b7q ftp://data.pdbj.org/pub/pdb/validation_reports/b7/5b7q | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 27235.615 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 6-254 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeromonas hydrophila (bacteria) Strain: ATCC 7966 / DSM 30187 / JCM 1027 / KCTC 2358 / NCIMB 9240 Gene: mtnN-1, AHA_0953 / Production host: Escherichia coli (E. coli) References: UniProt: A0KGU9, methylthioadenosine nucleosidase, adenosylhomocysteine nucleosidase #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.06 % |
---|---|
Crystal grow | Temperature: 288 K / Method: evaporation / pH: 4.6 Details: 6% (w/v) polyethylene glycol 4000, 0.1 M sodium acetate trihydrate (pH 4.6) |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.903 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.903 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→24.25 Å / Num. obs: 115439 / % possible obs: 99.7 % / Redundancy: 12.7 % / Net I/σ(I): 19.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.493→24.25 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 15.81
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.493→24.25 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|