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Yorodumi- PDB-3ci4: Structure of the PduO-type ATP:co(I)rrinoid adenosyltransferase f... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ci4 | ||||||
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Title | Structure of the PduO-type ATP:co(I)rrinoid adenosyltransferase from Lactobacillus reuteri complexed with four-coordinate cob(II)inamide and ATP | ||||||
Components | Cobalamin adenosyltransferase PduO-like protein | ||||||
Keywords | TRANSFERASE / adenosyltransferase variant / ATP binding / corrin binding | ||||||
Function / homology | Function and homology information corrinoid adenosyltransferase / corrinoid adenosyltransferase activity / cobalamin biosynthetic process / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Lactobacillus reuteri (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Maurice, M.St. / Mera, P.E. / Escalante-Semerena, J.C. / Rayment, I. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Structural characterization of a human-type corrinoid adenosyltransferase confirms that coenzyme B12 is synthesized through a four-coordinate intermediate. Authors: St Maurice, M. / Mera, P. / Park, K. / Brunold, T.C. / Escalante-Semerena, J.C. / Rayment, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ci4.cif.gz | 58.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ci4.ent.gz | 40.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ci4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ci4_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 3ci4_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 3ci4_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 3ci4_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/3ci4 ftp://data.pdbj.org/pub/pdb/validation_reports/ci/3ci4 | HTTPS FTP |
-Related structure data
-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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 22382.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lactobacillus reuteri (bacteria) / Strain: CRL1098 / Gene: cobA / Plasmid: pET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q50EJ2, corrinoid adenosyltransferase |
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-Non-polymers , 5 types, 89 molecules
#2: Chemical | ChemComp-K / |
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#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-ATP / |
#5: Chemical | ChemComp-CBY / |
#6: 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: 2.2 Å3/Da / Density % sol: 44.1 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion / pH: 6 Details: ANOXIC, 13% PEG 8000, 0.1 M MES, 200 mM KCl, 33 ug/mL FMN reductase, 20 mM NADH, 2 mM FMN, 2 mM dicyanocobinamide, 2 mM MgCl2, 2 mM ATP, pH 6, VAPOR DIFFUSION, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: May 25, 2007 / Details: Montel |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 13603 / % possible obs: 98.2 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 5.7 |
Reflection shell | Highest resolution: 2 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 1.7 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.898 / SU B: 3.579 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.194 / ESU R Free: 0.159 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 8.122 Å2
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Refine analyze | Luzzati coordinate error obs: 0.191 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 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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