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Yorodumi- PDB-1y8c: Crystal structure of a S-adenosylmethionine-dependent methyltrans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y8c | ||||||
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Title | Crystal structure of a S-adenosylmethionine-dependent methyltransferase from Clostridium acetobutylicum ATCC 824 | ||||||
Components | S-adenosylmethionine-dependent methyltransferase | ||||||
Keywords | TRANSFERASE / Structural Genomics / Protein Structure Initiative / PSI / NYSGXRC / New York SGX Research Center for Structural Genomics / T1987 / CAC2371 / methyltransferase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Clostridium acetobutylicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Rajashankar, K.R. / Kniewel, R. / Lee, K. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a S-adenosylmethionine-dependent methyltransferase from Clostridium acetobutylicum ATCC 824 Authors: Rajashankar, K.R. / Kniewel, R. / Lee, K. / Lima, C.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y8c.cif.gz | 65.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y8c.ent.gz | 47.9 KB | Display | PDB format |
PDBx/mmJSON format | 1y8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y8/1y8c ftp://data.pdbj.org/pub/pdb/validation_reports/y8/1y8c | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 29331.541 Da / Num. of mol.: 1 / Fragment: SAM dependent methyltransferase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Strain: ATCC 824 / Gene: CAC2371, 1118554 / Plasmid: PET T7 / Production host: Escherichia coli (E. coli) / Strain (production host): B834, DE3 / References: UniProt: Q97GJ5 |
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#2: Chemical | ChemComp-SO4 / |
#3: 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: 3 Å3/Da / Density % sol: 58.64 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 3.6M Ammonium Sulfate, 0.1M Potassium Phosphate Monobasic, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTAM Q315 / Detector: CCD / Date: Nov 6, 2004 Details: Vertical focussing mirror down stream of monochromator |
Radiation | Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 23695 / Num. obs: 23695 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 37.3 Å2 / Rsym value: 0.057 / Net I/σ(I): 22.7 |
Reflection shell | Resolution: 2.5→2.59 Å / Num. unique all: 2307 / Rsym value: 0.362 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→44.27 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 359501.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: No clear density was observed for Tyr4 side chain. Hence it was modelled as Ser.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.4609 Å2 / ksol: 0.375655 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→44.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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