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Yorodumi- PDB-4e31: X-ray Structure of the Y76F mutant of TcaB9, a C-3'-Methyltransfe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4.0E+31 | ||||||
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Title | X-ray Structure of the Y76F mutant of TcaB9, a C-3'-Methyltransferase, in Complex with S-Adenosyl-L-Homocysteine and Sugar Product | ||||||
Components | TcaB9 | ||||||
Keywords | TRANSFERASE / kijanose / tetronitrose / tetradeoxy sugar / keto sugar / sugar methylation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Micromonospora chalcea (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Bruender, N.A. / Holden, H.M. | ||||||
Citation | Journal: Protein Sci. / Year: 2012 Title: Probing the catalytic mechanism of a C-3'-methyltransferase involved in the biosynthesis of D-tetronitrose. Authors: Bruender, N.A. / Holden, H.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e31.cif.gz | 108.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e31.ent.gz | 79.4 KB | Display | PDB format |
PDBx/mmJSON format | 4e31.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4e31_validation.pdf.gz | 1001.7 KB | Display | wwPDB validaton report |
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Full document | 4e31_full_validation.pdf.gz | 1005.9 KB | Display | |
Data in XML | 4e31_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 4e31_validation.cif.gz | 33.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/4e31 ftp://data.pdbj.org/pub/pdb/validation_reports/e3/4e31 | HTTPS FTP |
-Related structure data
Related structure data | 4e2wC 4e2xC 4e2yC 4e2zC 4e30C 4e32C 4e33C 3ndjS 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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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 46074.914 Da / Num. of mol.: 1 / Mutation: Y76F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micromonospora chalcea (bacteria) / Gene: tcab9 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 DE3 References: UniProt: B5L6K6, Transferases; Transferring one-carbon groups; Methyltransferases |
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-Non-polymers , 5 types, 431 molecules
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-SAH / | #5: Chemical | ChemComp-JHZ / ( | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.96 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.2-1.6 M sodium/potassium phosphate, 10 mM dTMP, 5 mM S-adenosyl-L-homocysteine, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Dec 31, 2011 / Details: Montel |
Radiation | Monochromator: nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→34 Å / Num. all: 45134 / Num. obs: 43793 / % possible obs: 97 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.75→1.85 Å / Redundancy: 1.86 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 2.69 / Num. unique all: 6335 / Rsym value: 0.255 / % possible all: 92.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3NDJ Resolution: 1.75→34 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.186 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.446 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
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