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Yorodumi- PDB-6pt8: Crystal Structure of CobT from Methanocaldococcus jannaschii in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pt8 | ||||||
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Title | Crystal Structure of CobT from Methanocaldococcus jannaschii in complex with Adenine Alpha-Ribotide and Nicotinic Acid | ||||||
Components | UPF0284 protein MJ1598 | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase, archaeal type / Phosphoribosyltransferase / nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase / Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase-like superfamily / ALPHA-ADENOSINE MONOPHOSPHATE / NICOTINIC ACID / PHOSPHATE ION / UPF0284 protein MJ1598 Function and homology information | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Schwarzwalder, A.H. / Jeter, V.L. / Vecellio, A.A. / Erpenbach, E. / Escalante, J.C. / Rayment, I. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Rep / Year: 2022 Title: Structural studies of the phosphoribosyltransferase involved in cobamide biosynthesis in methanogenic archaea and cyanobacteria. Authors: Jeter, V.L. / Schwarzwalder, A.H. / Rayment, I. / Escalante-Semerena, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pt8.cif.gz | 275.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pt8.ent.gz | 222.5 KB | Display | PDB format |
PDBx/mmJSON format | 6pt8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pt/6pt8 ftp://data.pdbj.org/pub/pdb/validation_reports/pt/6pt8 | HTTPS FTP |
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-Related structure data
Related structure data | 6ptfC 6pu6C 3l0zS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 37847.953 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea) Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: MJ1598 / Production host: Escherichia coli (E. coli) / References: UniProt: Q58993 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.06 Å3/Da / Density % sol: 40.37 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: Crystals formed by mixing 1:1 ratio of 13.3 mg/mL protein solution with well solution containing 100 mM 4-(2-Hydroxyethyl)-1-piperazinepropanesulfonic acid (HEPPS) pH 8.5 and 22% (w/v) PEG ...Details: Crystals formed by mixing 1:1 ratio of 13.3 mg/mL protein solution with well solution containing 100 mM 4-(2-Hydroxyethyl)-1-piperazinepropanesulfonic acid (HEPPS) pH 8.5 and 22% (w/v) PEG 8K. 1 mM adenine and 50 mM Sodium/Potassium Phosphate pH 7.0 were added to protein prior to mixing with well solution. Substrates were captured in lattice prior to freezing by soaking crystals in 20% (w/v) ethylene glycol, 100 mM HEPPS pH 8.5, 22% (w/v) PEG 8K, 25 mM sodium/potassium phosophate pH 7.0, 1 mM nicotinic acid mononucleotide, and 1 mM adenine for 30 minutes. Crystals were then soaked in the same solution, but with 30% PEG 8K instead of 20% ethylene glycol and 20% PEG 8K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Aug 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→41.973 Å / Num. obs: 118689 / % possible obs: 98.95 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.09626 / Net I/σ(I): 12.18 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.6674 / Mean I/σ(I) obs: 2.92 / Num. unique obs: 11857 / % possible all: 98.98 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3L0Z Resolution: 1.4→41.973 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.66
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.57 Å2 / Biso mean: 18.8823 Å2 / Biso min: 6.36 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.4→41.973 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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