[English] 日本語
Yorodumi- PDB-1vjt: Crystal structure of Alpha-glucosidase (TM0752) from Thermotoga m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vjt | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Alpha-glucosidase (TM0752) from Thermotoga maritima at 2.50 A resolution | ||||||
Components | alpha-glucosidase | ||||||
Keywords | HYDROLASE / TM0752 / ALPHA-GLUCOSIDASE / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics | ||||||
Function / homology | Function and homology information oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Thermotoga maritima (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of Alpha-glucosidase (TM0752) from Thermotoga maritima at 2.50 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
| ||||||
Remark 600 | HETEROGEN THE NICOTINAMIDE MOIETY OF NAD WAS NOT VISIBLE IN THE DENSITY. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1vjt.cif.gz | 106.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1vjt.ent.gz | 84.7 KB | Display | PDB format |
PDBx/mmJSON format | 1vjt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vjt_validation.pdf.gz | 719.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1vjt_full_validation.pdf.gz | 725.9 KB | Display | |
Data in XML | 1vjt_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 1vjt_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/1vjt ftp://data.pdbj.org/pub/pdb/validation_reports/vj/1vjt | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 57599.273 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0752 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZL1, EC: 3.2.1.139 |
---|---|
#2: Chemical | ChemComp-NAD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 47.87 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 8.1 Details: 0.2M tri-lithium citrate tetrahydrate, 20% PEG-3350, pH 8.1, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.00000, 0.979340, 0.979206 | ||||||||||||
Detector | Type: APS / Detector: CCD / Date: Aug 8, 2003 | ||||||||||||
Radiation | Monochromator: Rosenbaum-Rock monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 15162 / % possible obs: 83.34 % / Redundancy: 3.12 % / Biso Wilson estimate: 44.23 Å2 / Rsym value: 0.057 / Net I/σ(I): 19.08 | ||||||||||||
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 2.03 % / Mean I/σ(I) obs: 3.11 / Num. unique all: 758 / Rsym value: 0.264 / % possible all: 42.11 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 2.5→43.64 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.878 / SU B: 22.539 / SU ML: 0.237 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.362 Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THE NICOTINAMIDE MOIETY OF NAD WAS NOT VISIBLE IN THE DENSITY. 3. RESIDUAL POSITIVE DIFFERENCE DENSITY LIES CLOSE TO THE SIDECHAINS OF ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THE NICOTINAMIDE MOIETY OF NAD WAS NOT VISIBLE IN THE DENSITY. 3. RESIDUAL POSITIVE DIFFERENCE DENSITY LIES CLOSE TO THE SIDECHAINS OF THE ACTIVE SITE RESIDUES SER10 AND PHE13.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 26.232 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→43.64 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.495→2.56 Å / Total num. of bins used: 20
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 59.5753 Å / Origin y: 9.3396 Å / Origin z: 21.7988 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection: ALL |