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Yorodumi- PDB-3t0c: Crystal structure of Streptococcus mutans MetE complexed with Zinc -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t0c | |||||||||
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Title | Crystal structure of Streptococcus mutans MetE complexed with Zinc | |||||||||
Components | 5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase | |||||||||
Keywords | TRANSFERASE / MetE / Barrel / methyltransferase | |||||||||
Function / homology | Function and homology information 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase / 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity / methionine synthase activity / 'de novo' L-methionine biosynthetic process / methylation / zinc ion binding / extracellular region / cytosol Similarity search - Function | |||||||||
Biological species | Streptococcus mutans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.187 Å | |||||||||
Authors | Fu, T.M. / Liang, Y.H. / Su, X.D. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Crystal Structures of Cobalamin-Independent Methionine Synthase (MetE) from Streptococcus mutans: A Dynamic Zinc-Inversion Model Authors: Fu, T.M. / Almqvist, J. / Liang, Y.H. / Li, L. / Huang, Y. / Su, X.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t0c.cif.gz | 168.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t0c.ent.gz | 125.7 KB | Display | PDB format |
PDBx/mmJSON format | 3t0c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t0c_validation.pdf.gz | 439.7 KB | Display | wwPDB validaton report |
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Full document | 3t0c_full_validation.pdf.gz | 447.5 KB | Display | |
Data in XML | 3t0c_validation.xml.gz | 31.4 KB | Display | |
Data in CIF | 3t0c_validation.cif.gz | 46.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t0/3t0c ftp://data.pdbj.org/pub/pdb/validation_reports/t0/3t0c | HTTPS FTP |
-Related structure data
Related structure data | 3l7rC 2nq5S 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
#1: Protein | Mass: 87799.820 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: metE / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q8CWX6, 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase | ||||
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#2: Chemical | #3: Chemical | ChemComp-ZN / | #4: 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: 2.32 Å3/Da / Density % sol: 47.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2M Li2SO4, 0.1M HEPES, 25%(w/v) polyethylene glycerol 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: BRUKER SMART 6000 / Detector: CCD / Date: May 8, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.187→52.63 Å / Num. all: 40832 / Num. obs: 39151 / % possible obs: 95.88 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 3.31 % / Biso Wilson estimate: 20.74 Å2 |
Reflection shell | Resolution: 2.19→2.33 Å / Num. unique all: 6372 / % possible all: 77.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2NQ5 Resolution: 2.187→42.068 Å / Occupancy max: 1 / Occupancy min: 0.18 / FOM work R set: 0.7848 / SU ML: 0.35 / σ(F): 1.91 / Phase error: 28.48 / 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 / Bsol: 38.393 Å2 / ksol: 0.3 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.47 Å2 / Biso mean: 26.1002 Å2 / Biso min: 9.06 Å2
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Refinement step | Cycle: LAST / Resolution: 2.187→42.068 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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