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Yorodumi- PDB-5b3f: Crystal structure of phosphoribulokinase from Methanospirillum hu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5b3f | ||||||
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Title | Crystal structure of phosphoribulokinase from Methanospirillum hungatei | ||||||
Components | Phosphoribulokinase/uridine kinase | ||||||
Keywords | TRANSFERASE / Archaea / Kinase | ||||||
Function / homology | phosphoribulokinase / phosphoribulokinase activity / Phosphoribulokinase / Phosphoribulokinase/uridine kinase / Phosphoribulokinase / Uridine kinase family / carbohydrate metabolic process / P-loop containing nucleoside triphosphate hydrolase / ATP binding / Phosphoribulokinase Function and homology information | ||||||
Biological species | Methanospirillum hungatei JF-1 (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | ||||||
Authors | Matsumura, H. / Ashida, H. | ||||||
Citation | Journal: Nat Commun / Year: 2017 Title: A RuBisCO-mediated carbon metabolic pathway in methanogenic archaea Authors: Kono, T. / Mehrotra, S. / Endo, C. / Kizu, N. / Matusda, M. / Kimura, H. / Mizohata, E. / Inoue, T. / Hasunuma, T. / Yokota, A. / Matsumura, H. / Ashida, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5b3f.cif.gz | 136.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5b3f.ent.gz | 109.7 KB | Display | PDB format |
PDBx/mmJSON format | 5b3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b3/5b3f ftp://data.pdbj.org/pub/pdb/validation_reports/b3/5b3f | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39679.891 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanospirillum hungatei JF-1 (archaea) Strain: JF-1 / Gene: Mhun_0794 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2FUB5 #2: Chemical | ChemComp-SO4 / #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: 2.32 Å3/Da / Density % sol: 46.9 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.8 / Details: PEG4000, lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 9, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→34.02 Å / Num. obs: 24121 / % possible obs: 92.2 % / Redundancy: 2.9 % / Biso Wilson estimate: 34.8 Å2 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.5→2.54 Å / Rmerge(I) obs: 0.274 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→34.02 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 269892.21 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
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Solvent computation | Bsol: 40.3927 Å2 / ksol: 0.4 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.5 Å2
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Refine analyze |
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Refinement step | Cycle: 1 / Resolution: 2.5→34.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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