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Yorodumi- PDB-3ldu: The crystal structure of a possible methylase from Clostridium di... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ldu | ||||||
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Title | The crystal structure of a possible methylase from Clostridium difficile 630. | ||||||
Components | Putative methylase | ||||||
Keywords | TRANSFERASE / methylase / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG / Methyltransferase | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Clostridium difficile (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å | ||||||
Authors | Tan, K. / Wu, R. / Buck, K. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
Citation | Journal: To be Published Title: The crystal structure of a possible methylase from Clostridium difficile 630. Authors: Tan, K. / Wu, R. / Buck, K. / Joachimiak, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ldu.cif.gz | 169.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ldu.ent.gz | 140.2 KB | Display | PDB format |
PDBx/mmJSON format | 3ldu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ldu_validation.pdf.gz | 795.8 KB | Display | wwPDB validaton report |
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Full document | 3ldu_full_validation.pdf.gz | 803.2 KB | Display | |
Data in XML | 3ldu_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 3ldu_validation.cif.gz | 27.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/3ldu ftp://data.pdbj.org/pub/pdb/validation_reports/ld/3ldu | HTTPS FTP |
-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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Details | Experimentally unknown. The molecule is likely a monomer. |
-Components
#1: Protein | Mass: 45110.254 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD1780 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q186Y7 | ||||
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#2: Chemical | ChemComp-GTP / | ||||
#3: Chemical | #4: Chemical | ChemComp-GOL / #5: 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: 2.14 Å3/Da / Density % sol: 42.64 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M MES, 15% PEG 400, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 20, 2009 / Details: mirror |
Radiation | Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→23.8 Å / Num. all: 41197 / Num. obs: 41197 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 35.9 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.807 / Mean I/σ(I) obs: 1.88 / Num. unique all: 2058 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.7→23.795 Å / SU ML: 0.23 / σ(F): 0 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.05 Å2 / ksol: 0.421 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→23.795 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Selection details: chain A not resid 62:155 |