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Yorodumi- PDB-3zo9: The structure of Trehalose Synthase (TreS) of Mycobacterium smegmatis -
+Open data
-Basic information
Entry | Database: PDB / ID: 3zo9 | ||||||
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Title | The structure of Trehalose Synthase (TreS) of Mycobacterium smegmatis | ||||||
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: 1.84 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 |
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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 |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zo9.cif.gz | 261.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zo9.ent.gz | 208.6 KB | Display | PDB format |
PDBx/mmJSON format | 3zo9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3zo9_validation.pdf.gz | 436.2 KB | Display | wwPDB validaton report |
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Full document | 3zo9_full_validation.pdf.gz | 445.5 KB | Display | |
Data in XML | 3zo9_validation.xml.gz | 51 KB | Display | |
Data in CIF | 3zo9_validation.cif.gz | 76.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zo/3zo9 ftp://data.pdbj.org/pub/pdb/validation_reports/zo/3zo9 | HTTPS FTP |
-Related structure data
Related structure data | 3zoaC 2ze0S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9758, 0.2179, 0.0196), Vector: |
-Components
#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: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.22 Å3/Da / Density % sol: 62 % / Description: NONE |
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Crystal grow | Details: 0.1 M SODIUM CACODYLATE BUFFER PH 6.5, 0.2 M MGCL2, 10% PEG 1000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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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: 1.84→35 Å / Num. obs: 139127 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 27.82 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.4 |
Reflection shell | Resolution: 1.84→1.89 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.05 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZE0 Resolution: 1.84→34.918 Å / SU ML: 0.17 / σ(F): 1.99 / Phase error: 19.39 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.84→34.918 Å
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Refine LS restraints |
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LS refinement shell |
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