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Yorodumi- PDB-3c48: Structure of the retaining glycosyltransferase MshA: The first st... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c48 | ||||||
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Title | Structure of the retaining glycosyltransferase MshA: The first step in mycothiol biosynthesis. Organism: Corynebacterium glutamicum- APO (OPEN) structure. | ||||||
Components | Predicted glycosyltransferases | ||||||
Keywords | TRANSFERASE / retaining glycosyltransferase / beta alpha beta / substrate assisted catalysis | ||||||
Function / homology | Function and homology information D-inositol-3-phosphate glycosyltransferase / D-inositol-3-phosphate glycosyltransferase activity / mycothiol biosynthetic process / UDP-sulfoquinovose:DAG sulfoquinovosyltransferase activity / sulfolipid biosynthetic process / glycolipid biosynthetic process / acetylglucosaminyltransferase activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | Corynebacterium glutamicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 2.1 Å | ||||||
Authors | Vetting, M.W. / Frantom, P.A. / Blanchard, J.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Structural and Enzymatic Analysis of MshA from Corynebacterium glutamicum: SUBSTRATE-ASSISTED CATALYSIS Authors: Vetting, M.W. / Frantom, P.A. / Blanchard, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c48.cif.gz | 172.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c48.ent.gz | 135.8 KB | Display | PDB format |
PDBx/mmJSON format | 3c48.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c48_validation.pdf.gz | 457.7 KB | Display | wwPDB validaton report |
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Full document | 3c48_full_validation.pdf.gz | 468.8 KB | Display | |
Data in XML | 3c48_validation.xml.gz | 33.2 KB | Display | |
Data in CIF | 3c48_validation.cif.gz | 48.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/3c48 ftp://data.pdbj.org/pub/pdb/validation_reports/c4/3c48 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 47892.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: MshA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) References: UniProt: Q8NTA6, Transferases; Glycosyltransferases; Hexosyltransferases #2: Chemical | ChemComp-SO4 / #3: 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: 2.84 Å3/Da / Density % sol: 56.74 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 8.5 Details: Protein (15 mg/ml, 400 mM Ammonium sulfate, 10% glycerol, 0.5 mM EDTA, 1 mM BME): Precipitant (20% Peg4000, 100 mM Tris pH 8.5, 200 mm LiSO4), Vapor diffusion under oil, temperature 291K, VAPOR DIFFUSION |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 1, 2007 |
Radiation | Monochromator: MSC Confocal Blue Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→35 Å / Num. all: 178087 / Num. obs: 60789 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 35.7 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 2.9 / Num. unique all: 8239 / Rsym value: 0.238 / % possible all: 91.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→34.53 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.904 / SU ML: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.177 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.496 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→34.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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