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Yorodumi- PDB-3dh0: Crystal structure of a SAM dependent methyltransferase from Aquif... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dh0 | ||||||
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Title | Crystal structure of a SAM dependent methyltransferase from Aquifex aeolicus | ||||||
Components | SAM dependent methyltransferase | ||||||
Keywords | TRANSFERASE / Cystal structure / PSI-2 / NYSGXRC / 11116c / SAM dependent / methyltransferase / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.72 Å | ||||||
Authors | Agarwal, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a SAM dependent methyltransferase from Aquifex aeolicus Authors: Agarwal, R. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dh0.cif.gz | 88.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dh0.ent.gz | 67.2 KB | Display | PDB format |
PDBx/mmJSON format | 3dh0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/3dh0 ftp://data.pdbj.org/pub/pdb/validation_reports/dh/3dh0 | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 25152.061 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_1457 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIPL / References: UniProt: O67440 #2: Chemical | #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: 2.29 Å3/Da / Density % sol: 46.19 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris pH 8.5, 2M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 8, 2008 / Details: mirrors |
Radiation | Monochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.72→50 Å / Num. all: 12492 / Num. obs: 12492 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Biso Wilson estimate: 60.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.72→2.82 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2 / Num. unique all: 1209 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD Starting model: None Resolution: 2.72→40.34 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 106026.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 32.9192 Å2 / ksol: 0.357554 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.72→40.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.72→2.89 Å / Rfactor Rfree error: 0.066 / Total num. of bins used: 6
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Xplor file |
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