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Yorodumi- PDB-6xxg: Structure of truncated 1-deoxy-D-xylulose 5-phosphate synthase (D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xxg | ||||||
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Title | Structure of truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Deinococcus radiodurans | ||||||
Components | 1-deoxy-D-xylulose-5-phosphate synthase,1-deoxy-D-xylulose-5-phosphate synthase | ||||||
Keywords | TRANSFERASE | ||||||
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: 2.099 Å | ||||||
Authors | Gierse, R.M. / Reddem, E. / Grooves, M.R. | ||||||
Funding support | Netherlands, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2021 Title: Identification of a 1-deoxy-D-xylulose-5-phosphate synthase (DXS) mutant with improved crystallographic properties. Authors: Gierse, R.M. / Reddem, E.R. / Alhayek, A. / Baitinger, D. / Hamid, Z. / Jakobi, H. / Laber, B. / Lange, G. / Hirsch, A.K.H. / Groves, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xxg.cif.gz | 404.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xxg.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6xxg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xxg_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 6xxg_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 6xxg_validation.xml.gz | 42.7 KB | Display | |
Data in CIF | 6xxg_validation.cif.gz | 62.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xx/6xxg ftp://data.pdbj.org/pub/pdb/validation_reports/xx/6xxg | HTTPS FTP |
-Related structure data
Related structure data | 2o1xS 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
#1: Protein | Mass: 63398.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: A loop of the native gene was deleted between amino acid 201 and 243. It was replaced with 7xG. more details in the related publication.,A loop of the native gene was deleted between amino ...Details: A loop of the native gene was deleted between amino acid 201 and 243. It was replaced with 7xG. more details in the related publication.,A loop of the native gene was deleted between amino acid 201 and 243. It was replaced with 7xG. more details in the related publication. Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant) Gene: dxs, DR_1475 / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9RUB5, 1-deoxy-D-xylulose-5-phosphate synthase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CA / #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: 2.27 Å3/Da / Density % sol: 45.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M Calcium acetate hydrate, 0.1 M Tris, 20 % PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 15, 2017 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.099→47.549 Å / Num. obs: 67987 / % possible obs: 99.08 % / Redundancy: 2 % / CC1/2: 0.913 / Net I/σ(I): 5.87 |
Reflection shell | Resolution: 2.1→2.175 Å / Num. unique obs: 6677 / CC1/2: 0.444 / % possible all: 99.48 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2o1x Resolution: 2.099→47.549 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.212 / WRfactor Rwork: 0.166 / Average fsc free: 0.8887 / Average fsc work: 0.9025 / Cross valid method: FREE R-VALUE / ESU R: 0.227 / ESU R Free: 0.188 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.734 Å2
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Refinement step | Cycle: LAST / Resolution: 2.099→47.549 Å
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Refine LS restraints |
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LS refinement shell |
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