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Yorodumi- PDB-3c4q: Structure of the retaining glycosyltransferase MshA : The first s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c4q | ||||||
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Title | Structure of the retaining glycosyltransferase MshA : The first step in mycothiol biosynthesis. Organism : Corynebacterium glutamicum- Complex with UDP | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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 | 3c4q.cif.gz | 165 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c4q.ent.gz | 130.6 KB | Display | PDB format |
PDBx/mmJSON format | 3c4q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c4q_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3c4q_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3c4q_validation.xml.gz | 30.7 KB | Display | |
Data in CIF | 3c4q_validation.cif.gz | 42.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/3c4q ftp://data.pdbj.org/pub/pdb/validation_reports/c4/3c4q | HTTPS FTP |
-Related structure data
Related structure data | 3c48SC 3c4vC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 46792.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: MshA / Plasmid: pET29 / Production host: Escherichia coli (E. coli) References: UniProt: Q8NTA6, Transferases; Glycosyltransferases; Hexosyltransferases #2: Chemical | #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: 4.2 Å3/Da / Density % sol: 70.73 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 5.5 Details: Protein (40 mg/ml, 400 mM Ammonium sulfate, 10% glycerol, 0.5 mM EDTA, 1 mM BME, 10 mM UDPNAG) Precipitant (0.8 M sodium citrate pH 5.5 ), Vapor diffusion under oil, temperature 298K, VAPOR DIFFUSION |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9778 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 1, 2007 Details: Meridionally-bent fused silica mirror with palladium and uncoated stripes |
Radiation | Monochromator: Double silicon(111) crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9778 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→80 Å / Num. all: 37594 / Num. obs: 37594 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 69.2 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 22.4 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 3.9 / Num. unique all: 5474 / Rsym value: 0.318 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3C48 Resolution: 2.8→78.25 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.927 / SU B: 20.121 / SU ML: 0.189 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.4 / ESU R Free: 0.262 / 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: 28.568 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→78.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.873 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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