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- PDB-3hm2: Crystal Structure of Putative Precorrin-6Y C5,15-Methyltransferas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3hm2 | ||||||
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Title | Crystal Structure of Putative Precorrin-6Y C5,15-Methyltransferase Targeted Domain from Corynebacterium diphtheriae | ||||||
![]() | precorrin-6Y C5,15-methyltransferase | ||||||
![]() | TRANSFERASE / alpha-beta-sandwich / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Methyltransferase | ||||||
Function / homology | ![]() protein methyltransferase activity / cobalamin biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, Y. / Bigelow, L. / Keigher, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG) | ||||||
![]() | ![]() Title: Crystal Structure of Putative Precorrin-6Y C5,15-Methyltransferase Targeted Domain from Corynebacterium diphtheriae Authors: Kim, Y. / Bigelow, L. / Keigher, L. / Joachimiak, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 265.1 KB | Display | ![]() |
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PDB format | ![]() | 225.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 513.6 KB | Display | ![]() |
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Full document | ![]() | 591.4 KB | Display | |
Data in XML | ![]() | 60.8 KB | Display | |
Data in CIF | ![]() | 83.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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Links
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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: 19190.488 Da / Num. of mol.: 8 / Fragment: residues 236-410 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.62 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2 M Calcium acetate hydrate 20 %w/v Polyethylene glycol 3,350, pH ----, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2009 / Details: mirrors |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→47.24 Å / Num. all: 72372 / Num. obs: 72372 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 6.4 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.3 / Num. unique all: 3635 / % possible all: 97.4 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.84 Å2 / ksol: 0.316 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.205→47.238 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / % reflection obs: 98 %
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