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Yorodumi- PDB-3gu3: Crystal Structure of the methyltransferase BC_2162 in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gu3 | ||||||
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Title | Crystal Structure of the methyltransferase BC_2162 in complex with S-Adenosyl-L-Homocysteine from Bacillus cereus, Northeast Structural Genomics Consortium Target BcR20 | ||||||
Components | Methyltransferase | ||||||
Keywords | TRANSFERASE / alpha-beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Methyltransferase | ||||||
Function / homology | Function and homology information Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation Similarity search - Function | ||||||
Biological species | Bacillus cereus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Forouhar, F. / Neely, H. / Seetharaman, J. / Ciano, C. / Ma, L. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. ...Forouhar, F. / Neely, H. / Seetharaman, J. / Ciano, C. / Ma, L. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Northeast Structural Genomics Consortium Target BcR20 Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Ciano, C. / Ma, L. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gu3.cif.gz | 125.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gu3.ent.gz | 103.8 KB | Display | PDB format |
PDBx/mmJSON format | 3gu3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/3gu3 ftp://data.pdbj.org/pub/pdb/validation_reports/gu/3gu3 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 32935.184 Da / Num. of mol.: 2 / Fragment: BC_2162 Mutation: Substitution of Met residues by Seleno-Met residues and addition of a C-tag (lehhhhhh). Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / Gene: BC_2162 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic References: UniProt: Q81E32, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | #3: Chemical | #4: 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: 4.43 Å3/Da / Density % sol: 72.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4 Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), and 10mM S-Adenosyl-L-Methionine . Reservoir solution: 100 mM Sodium Citrate and 5.76M Potassium Acetate , VAPOR ...Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), and 10mM S-Adenosyl-L-Methionine . Reservoir solution: 100 mM Sodium Citrate and 5.76M Potassium Acetate , VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97905 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 10, 2007 / Details: Mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97905 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 100547 / Num. obs: 100246 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.066 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.98 / Num. unique all: 10106 / Rsym value: 0.479 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→19.92 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 314365.531 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.8 Å2 / ksol: 0.45 e/Å3 | ||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 10
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