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Yorodumi- PDB-2gh1: Crystal Structure of the putative SAM-dependent methyltransferase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2gh1 | ||||||
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Title | Crystal Structure of the putative SAM-dependent methyltransferase BC2162 from Bacillus cereus, Northeast Structural Genomics Target BcR20. | ||||||
Components | Methyltransferase | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta protein / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG | ||||||
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: 2.5 Å | ||||||
Authors | Forouhar, F. / Neely, H. / Jayaraman, S. / Ciao, M. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal Structure of the putative SAM-dependent methyltransferase BC2162 from Bacillus cereus, Northeast Structural Genomics Target BcR20. Authors: Forouhar, F. / Neely, H. / Jayaraman, S. / Ciao, M. / Xiao, R. / Acton, T.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 | 2gh1.cif.gz | 123.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2gh1.ent.gz | 103.5 KB | Display | PDB format |
PDBx/mmJSON format | 2gh1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gh/2gh1 ftp://data.pdbj.org/pub/pdb/validation_reports/gh/2gh1 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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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: 35113.477 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / Gene: BC2162, GeneID:1204511 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q81E32 #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: 4.15 Å3/Da / Density % sol: 70.38 % |
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Crystal grow | Temperature: 277 K / Method: microbatch / pH: 4 Details: 100 mM Sodium Citrate, 5.76M Potassium Acetate, and 5 mM DTT. , pH 4.0, Microbatch., temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9795 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 18, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→29.75 Å / Num. all: 39116 / Num. obs: 38921 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.088 / Net I/σ(I): 12.29 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3921 / Rsym value: 0.534 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→29.75 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 230779.42 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / 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: 44.1419 Å2 / ksol: 0.381537 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.4 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→29.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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