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Yorodumi- PDB-2oek: Crystal structure of a rubisco-like protein from Geobacillus kaus... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2oek | ||||||
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Title | Crystal structure of a rubisco-like protein from Geobacillus kaustophilus liganded with Mg2+ ions | ||||||
Components | 2,3-diketo-5-methylthiopentyl-1-phosphate enolase | ||||||
Keywords | ISOMERASE / Rubisco-like protein / "enolase" | ||||||
Function / homology | Function and homology information 2,3-diketo-5-methylthiopentyl-1-phosphate enolase / 2,3-diketo-5-methylthiopentyl-1-phosphate enolase activity / L-methionine salvage from S-adenosylmethionine / L-methionine salvage from methylthioadenosine / carbon fixation / ribulose-bisphosphate carboxylase activity / magnesium ion binding Similarity search - Function | ||||||
Biological species | Geobacillus kaustophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Fedorov, A.A. / Imker, H.J. / Fedorov, E.V. / Almo, S.C. / Gerlt, J.A. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Mechanistic Diversity in the RuBisCO Superfamily: The "Enolase" in the Methionine Salvage Pathway in Geobacillus kaustophilus. Authors: Imker, H.J. / Fedorov, A.A. / Fedorov, E.V. / Almo, S.C. / Gerlt, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oek.cif.gz | 182.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oek.ent.gz | 143.1 KB | Display | PDB format |
PDBx/mmJSON format | 2oek.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/2oek ftp://data.pdbj.org/pub/pdb/validation_reports/oe/2oek | HTTPS FTP |
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-Related structure data
Related structure data | 2oejC 2oelC 2oemC 20ejS C: citing same article (ref.) 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 on special symmetry positions |
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Details | The biological assembly is a dimer AB |
-Components
#1: Protein | Mass: 45003.551 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Gene: mtnW / Production host: Escherichia coli (E. coli) References: UniProt: Q5L1E2, Isomerases; Intramolecular oxidoreductases; Interconverting keto- and enol-groups #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: 2.3 Å3/Da / Density % sol: 46.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 24%peg 3350, 0.1 M tris-HCl, 0.2 M ammonium acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 30, 2006 / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25 Å / Num. all: 74695 / Num. obs: 74695 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 11.9 Å2 / Rmerge(I) obs: 0.044 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 20EJ Resolution: 1.8→24.83 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 232409.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.1443 Å2 / ksol: 0.364665 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→24.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.86 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
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Xplor file |
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