[English] 日本語
Yorodumi- PDB-3zoa: The structure of Trehalose Synthase (TreS) of Mycobacterium smegm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zoa | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The structure of Trehalose Synthase (TreS) of Mycobacterium smegmatis in complex with acarbose | |||||||||
Components | TREHALOSE SYNTHASE/AMYLASE TRES | |||||||||
Keywords | HYDROLASE / GLYCOHYDROLASE / DRUG DESIGN / TUBERCULOSIS | |||||||||
Function / homology | Function and homology information trehalose metabolic process / maltose alpha-D-glucosyltransferase / maltose alpha-D-glucosyltransferase activity / maltose metabolic process / alpha-amylase / glycogen biosynthetic process / alpha-amylase activity / glycogen metabolic process / polysaccharide catabolic process / calcium ion binding Similarity search - Function | |||||||||
Biological species | MYCOBACTERIUM SMEGMATIS (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | |||||||||
Authors | Caner, S. / Nguyen, N. / Aguda, A. / Zhang, R. / Pan, Y.T. / Withers, S.G. / Brayer, G.D. | |||||||||
Citation | Journal: Glycobiology / Year: 2013 Title: The Structure of the Mycobacterium Smegmatis Trehalose Synthase Reveals an Unusual Active Site Configuration and Acarbose-Binding Mode. Authors: Caner, S. / Nguyen, N. / Aguda, A. / Zhang, R. / Pan, Y.T. / Withers, S.G. / Brayer, G.D. | |||||||||
History |
| |||||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3zoa.cif.gz | 262.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3zoa.ent.gz | 209.3 KB | Display | PDB format |
PDBx/mmJSON format | 3zoa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/3zoa ftp://data.pdbj.org/pub/pdb/validation_reports/zo/3zoa | HTTPS FTP |
---|
-Related structure data
Related structure data | 3zo9C 2ze0S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein / Sugars , 2 types, 3 molecules AB
#1: Protein | Mass: 68272.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) MYCOBACTERIUM SMEGMATIS (bacteria) References: UniProt: A0R6E0, alpha-amylase, maltose alpha-D-glucosyltransferase #2: Polysaccharide | 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D- ...4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-acarbose | |
---|
-Non-polymers , 4 types, 955 molecules
#3: Chemical | #4: Chemical | ChemComp-CL / #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 62 % / Description: NONE |
---|---|
Crystal grow | Details: 0.1 M SODIUM CACODYLATE BUFFER PH 6.5, 0.2 M MGCL2, 10% PEG 1000, 100 MM ACARBOSE |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 |
Detector | Type: DECTRIS PILATUS / Detector: PIXEL / Date: Jul 21, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→35 Å / Num. obs: 143054 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 27.09 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.83 / % possible all: 94 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZE0 Resolution: 1.85→34.816 Å / SU ML: 0.17 / σ(F): 1.99 / Phase error: 20.49 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→34.816 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|