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- PDB-7a9h: Truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Myco... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7a9h | ||||||
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Title | Truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Mycobacterium tuberculosis | ||||||
![]() | 1-deoxy-D-xylulose-5-phosphate synthase,1-deoxy-D-xylulose-5-phosphate synthase | ||||||
![]() | TRANSFERASE | ||||||
Function / homology | ![]() 1-deoxy-D-xylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase activity / 1-deoxy-D-xylulose 5-phosphate biosynthetic process / thiamine binding / chlorophyll biosynthetic process / thiamine biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / thiamine pyrophosphate binding / manganese ion binding ...1-deoxy-D-xylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase activity / 1-deoxy-D-xylulose 5-phosphate biosynthetic process / thiamine binding / chlorophyll biosynthetic process / thiamine biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / thiamine pyrophosphate binding / manganese ion binding / positive regulation of gene expression / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gierse, R.M. / Reddem, E. / Grooves, M.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: First crystal structures of 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Mycobacterium tuberculosis indicate a distinct mechanism of intermediate stabilization. Authors: Gierse, R.M. / Oerlemans, R. / Reddem, E.R. / Gawriljuk, V.O. / Alhayek, A. / Baitinger, D. / Jakobi, H. / Laber, B. / Lange, G. / Hirsch, A.K.H. / Groves, M.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 407.5 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 44.1 KB | Display | |
Data in CIF | ![]() | 65.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7a9gC ![]() 2o1xS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 66690.461 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: dxs, Rv2682c, MTCY05A6.03c / Plasmid: pETM-11 / Production host: ![]() ![]() References: UniProt: P9WNS3, 1-deoxy-D-xylulose-5-phosphate synthase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M DL-Malic acid, MES monohydrate, Tris (MMT)-buffer, pH 5.0 + 25% PEG1500 PH range: 5.0 + |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 3, 2017 / Details: double crystal monochromator |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033213 Å / Relative weight: 1 |
Reflection | Resolution: 1.849→43.832 Å / Num. obs: 93268 / % possible obs: 91 % / Redundancy: 1.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0233 / Rpim(I) all: 0.0233 / Net I/σ(I): 20.99 |
Reflection shell | Resolution: 1.85→1.916 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.0852 / Mean I/σ(I) obs: 6.54 / Num. unique obs: 6412 / CC1/2: 0.979 / Rpim(I) all: 0.0852 / % possible all: 62.53 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2o1x Resolution: 1.849→43.832 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.178 / WRfactor Rwork: 0.154 / Average fsc free: 0.9572 / Average fsc work: 0.9631 / Cross valid method: FREE R-VALUE / ESU R: 0.117 / ESU R Free: 0.105 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: 19.252 Å2
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Refinement step | Cycle: LAST / Resolution: 1.849→43.832 Å
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Refine LS restraints |
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LS refinement shell |
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