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Yorodumi- PDB-3t7t: Crystal structure of complex of SAH and BVU_3255, a methyltransfe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t7t | ||||||
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Title | Crystal structure of complex of SAH and BVU_3255, a methyltransferase from Bacteroides vulgatus ATCC 8482 | ||||||
Components | Putative methyltransferase | ||||||
Keywords | TRANSFERASE / Small molecule methyltransferase / BVU_3255 / ROSSMANN FOLD / METHYLTRASNFERASE / SAM / Methylation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacteroides vulgatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Kumar, V. / Sivaraman, J. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2011 Title: Structural characterization of BVU_3255, a methyltransferase from human intestine antibiotic resistant pathogen Bacteroides vulgatus Authors: Kumar, V. / Sivaraman, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t7t.cif.gz | 208.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t7t.ent.gz | 166.4 KB | Display | PDB format |
PDBx/mmJSON format | 3t7t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t7/3t7t ftp://data.pdbj.org/pub/pdb/validation_reports/t7/3t7t | HTTPS FTP |
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-Related structure data
Related structure data | 3t7rC 3t7sC 3e7pS 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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Unit cell |
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-Components
#1: Protein | Mass: 30664.715 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / Gene: BVU_3255 / Plasmid: pGS21a / Production host: Escherichia coli (E. coli) / Strain (production host): (DE3)BL21 / References: UniProt: A6L5C0 #2: Chemical | ChemComp-SAH / #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: 2.15 Å3/Da / Density % sol: 42.75 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 120mM (NH4)(NO3), 16% w/v PEG 3350, 200mM non-detergent sulfobetaine 221 (NDSB-221), VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-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 Platinum 135 / Detector: CCD / Date: Nov 30, 2010 |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 35718 / Num. obs: 35718 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.072 / Net I/σ(I): 10.42 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3E7P Resolution: 2.5→30 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 24.4665 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.82 Å2 / Biso mean: 31.8601 Å2 / Biso min: 4.71 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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Xplor file |
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