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Yorodumi- PDB-3ndc: Crystal structure of Precorrin-4 C11-methyltransferase from Rhodo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ndc | ||||||
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Title | Crystal structure of Precorrin-4 C11-methyltransferase from Rhodobacter capsulatus | ||||||
Components | Precorrin-4 C(11)-methyltransferase | ||||||
Keywords | TRANSFERASE / methyltransferase / SAH | ||||||
Function / homology | Function and homology information precorrin-4 C11-methyltransferase / precorrin-4 C11-methyltransferase activity / cobalamin biosynthetic process / methylation Similarity search - Function | ||||||
Biological species | Rhodobacter capsulatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Seyedarabi, A. / Pickersgill, R.W. | ||||||
Citation | Journal: To be Published Title: Crystal structure of Precorrin-4 C11-methyltransferase from Rhodobacter capsulatus Authors: Seyedarabi, A. / Pickersgill, R.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ndc.cif.gz | 104.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ndc.ent.gz | 79.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ndc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ndc_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3ndc_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3ndc_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 3ndc_validation.cif.gz | 29.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/3ndc ftp://data.pdbj.org/pub/pdb/validation_reports/nd/3ndc | HTTPS FTP |
-Related structure data
Related structure data | 1cbfS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28014.910 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodobacter capsulatus (bacteria) / Strain: SB1003 / Gene: cobM / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLysS References: UniProt: O68100, precorrin-4 C11-methyltransferase #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: 2.66 Å3/Da / Density % sol: 53.79 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M Hepes pH 7.5, 10% isopropanol, 20% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.117 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 15, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.117 Å / Relative weight: 1 |
Reflection | Resolution: 2→42.26 Å / Num. all: 39472 / Num. obs: 39472 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Biso Wilson estimate: 33.23 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.3 / Num. unique all: 5720 / Rsym value: 0.62 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CBF Resolution: 2→40.56 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.417 / SU ML: 0.098 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.142 / 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: 36.858 Å2
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Refinement step | Cycle: LAST / Resolution: 2→40.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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