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Yorodumi- PDB-3rsb: Structure of the Archaeal GTP:AdoCbi-P Guanylyltransferase (CobY)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rsb | ||||||
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Title | Structure of the Archaeal GTP:AdoCbi-P Guanylyltransferase (CobY) from Methanocaldococcus jannaschii | ||||||
Components | Adenosylcobinamide-phosphate guanylyltransferase | ||||||
Keywords | TRANSFERASE / Pyrophosphorylase binding motif / pyrophosphorylase | ||||||
Function / homology | Function and homology information adenosylcobinamide-phosphate guanylyltransferase / cobinamide phosphate guanylyltransferase activity / cobalamin biosynthetic process / nucleotidyltransferase activity / GTP binding Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å | ||||||
Authors | Newmister, S.A. / Otte, M.M. / Escalante-Semerena, J.C. / Rayment, I. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Structure and Mutational Analysis of the Archaeal GTP:AdoCbi-P Guanylyltransferase (CobY) from Methanocaldococcus jannaschii: Insights into GTP Binding and Dimerization. Authors: Newmister, S.A. / Otte, M.M. / 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 | 3rsb.cif.gz | 149.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rsb.ent.gz | 126.4 KB | Display | PDB format |
PDBx/mmJSON format | 3rsb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3rsb_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 3rsb_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 3rsb_validation.xml.gz | 43 KB | Display | |
Data in CIF | 3rsb_validation.cif.gz | 56.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rs/3rsb ftp://data.pdbj.org/pub/pdb/validation_reports/rs/3rsb | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 22109.893 Da / Num. of mol.: 4 / Mutation: G153D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: cobY, MJ1117 / Plasmid: pCobY14 / Production host: Escherichia coli (E. coli) References: UniProt: Q58517, adenosylcobinamide-phosphate guanylyltransferase #2: Chemical | ChemComp-GTP / #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: 2.94 Å3/Da / Density % sol: 58.13 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 60% 2-methyl-2,4-pentanediol, 0.1M 2-(N-morpholino)ethanesulfonic acid (MES), pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791 Å | ||||||||||||||||||||
Detector | Type: SBC-3 / Detector: CCD / Date: Nov 13, 2009 / Details: Mirrors | ||||||||||||||||||||
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | ||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.8→50 Å / Num. all: 24528 / Num. obs: 24528 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 31.6 | ||||||||||||||||||||
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 3.75 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.8→19.57 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.864 / SU B: 16.412 / SU ML: 0.33 / Cross valid method: THROUGHOUT / ESU R Free: 0.09 / 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: 47.48 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→19.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.872 Å / Total num. of bins used: 20
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