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Yorodumi- PDB-6ouw: 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Deinococcus r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ouw | |||||||||
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Title | 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Deinococcus radiodurans with enamine intermediate bound | |||||||||
Components | 1-deoxy-D-xylulose-5-phosphate synthase | |||||||||
Keywords | TRANSFERASE / 1-deoxy-D-xylulose 5-phosphate synthase / DXPS / thiamine diphosphate / thiamine pyrophosphate / ThDP / TPP / changes / the MEP pathway | |||||||||
Function / homology | Function and homology information 1-deoxy-D-xylulose-5-phosphate synthase / 1-deoxy-D-xylulose 5-phosphate biosynthetic process / 1-deoxy-D-xylulose-5-phosphate synthase activity / chlorophyll biosynthetic process / thiamine biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / thiamine pyrophosphate binding / magnesium ion binding / cytosol Similarity search - Function | |||||||||
Biological species | Deinococcus radiodurans (radioresistant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.398 Å | |||||||||
Authors | Chen, P.Y.-T. / Drennan, C.L. | |||||||||
Funding support | United States, 2items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: X-ray crystallography-based structural elucidation of enzyme-bound intermediates along the 1-deoxy-d-xylulose 5-phosphate synthase reaction coordinate. Authors: Chen, P.Y. / DeColli, A.A. / Freel Meyers, C.L. / Drennan, C.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ouw.cif.gz | 227.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ouw.ent.gz | 176.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ouw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ouw_validation.pdf.gz | 766.6 KB | Display | wwPDB validaton report |
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Full document | 6ouw_full_validation.pdf.gz | 768.2 KB | Display | |
Data in XML | 6ouw_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 6ouw_validation.cif.gz | 29.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/6ouw ftp://data.pdbj.org/pub/pdb/validation_reports/ou/6ouw | HTTPS FTP |
-Related structure data
Related structure data | 6ouvC 2o1xS 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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-Components
#1: Protein | Mass: 70029.508 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Gene: dxs, DR_1475 / Production host: Escherichia coli (E. coli) References: UniProt: Q9RUB5, 1-deoxy-D-xylulose-5-phosphate synthase |
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#2: Chemical | ChemComp-HTL / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-NA / |
#5: 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: 2.25 Å3/Da / Density % sol: 45.41 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, sitting drop Details: 0.10 M MOPSO, Bis-Tris pH 6.5, 12.5% (w/v) PEG 4000, 20% (w/v) 1,2,6-hexanetriol, 20 mM DL-arginine, 20 mM DL-threonine, 20 mM DL-histidine, 20 mM DL-5-hydroxylysine, and 20 mM trans-4-hydroxy-L-proline |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.398→49.4 Å / Num. obs: 23154 / % possible obs: 98.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.398→2.49 Å / Rmerge(I) obs: 0.42 / Num. unique obs: 2156 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2O1X Resolution: 2.398→49.388 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.96
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.398→49.388 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -26.2691 Å / Origin y: 27.6911 Å / Origin z: 23.1687 Å
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Refinement TLS group | Selection details: chain 'A' |