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Yorodumi- PDB-3njr: Crystal structure of C-terminal domain of precorrin-6Y C5,15-meth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3njr | ||||||
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Title | Crystal structure of C-terminal domain of precorrin-6Y C5,15-methyltransferase from Rhodobacter capsulatus | ||||||
Components | Precorrin-6y methylase | ||||||
Keywords | TRANSFERASE / methyltransferase / decarboxylase | ||||||
Function / homology | Function and homology information precorrin-6B C5,15-methyltransferase (decarboxylating) / precorrin-6Y C5,15-methyltransferase (decarboxylating) activity / protein methyltransferase activity / cobalamin biosynthetic process / Transferases; Transferring one-carbon groups; Methyltransferases Similarity search - Function | ||||||
Biological species | Rhodobacter capsulatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Seyedarabi, A. / Pickersgill, R.W. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2012 Title: An enzyme-trap approach allows isolation of intermediates in cobalamin biosynthesis. Authors: Deery, E. / Schroeder, S. / Lawrence, A.D. / Taylor, S.L. / Seyedarabi, A. / Waterman, J. / Wilson, K.S. / Brown, D. / Geeves, M.A. / Howard, M.J. / Pickersgill, R.W. / Warren, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3njr.cif.gz | 85.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3njr.ent.gz | 63.2 KB | Display | PDB format |
PDBx/mmJSON format | 3njr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nj/3njr ftp://data.pdbj.org/pub/pdb/validation_reports/nj/3njr | HTTPS FTP |
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-Related structure data
Related structure data | 4au1C 4fdvC 3hm2S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 22016.939 Da / Num. of mol.: 2 / Fragment: C-terminal domain, residues 214-396 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Strain: SB1003 / Gene: cobL / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLySs References: UniProt: O68099, UniProt: D5AV04*PLUS, precorrin-6B C5,15-methyltransferase (decarboxylating) #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PG4 / | #5: 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: 2.12 Å3/Da / Density % sol: 42.09 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1M tri-sodium citrate dihydrate pH 5.6, 20% isopropanol and 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.011 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.011 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→72.93 Å / Num. all: 10412 / Num. obs: 10402 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 5.3 / Rsym value: 0.214 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HM2 Resolution: 2.7→40.54 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.894 / SU B: 13.677 / SU ML: 0.288 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.688 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→40.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.701→2.771 Å / Total num. of bins used: 20
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