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Yorodumi- PDB-7a9g: Truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Myco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7a9g | ||||||
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Title | Truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Mycobacterium tuberculosis with intermediate 2-acetyl-thiamine diphosphate | ||||||
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 / 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 biosynthetic process / 1-deoxy-D-xylulose-5-phosphate synthase activity / 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 | Mycobacterium tuberculosis H37Rv (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Gierse, R.M. / Reddem, E. / Grooves, M.R. | ||||||
Funding support | Netherlands, 1items
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Citation | Journal: Sci Rep / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7a9g.cif.gz | 403.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a9g.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7a9g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7a9g_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7a9g_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7a9g_validation.xml.gz | 42.7 KB | Display | |
Data in CIF | 7a9g_validation.cif.gz | 61.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/7a9g ftp://data.pdbj.org/pub/pdb/validation_reports/a9/7a9g | HTTPS FTP |
-Related structure data
Related structure data | 7a9hC 2o1xS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AAABBB
#1: Protein | Mass: 70987.516 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Gene: dxs, Rv2682c, MTCY05A6.03c / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P9WNS3, 1-deoxy-D-xylulose-5-phosphate synthase |
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-Non-polymers , 8 types, 423 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-PEG / #5: Chemical | ChemComp-PGE / #6: Chemical | #7: Chemical | ChemComp-GOL / | #8: Chemical | ChemComp-PO4 / | #9: Water | ChemComp-HOH / | |
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-Details
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: 2.26 Å3/Da / Density % sol: 45.47 % |
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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: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033213 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 18, 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: 1.9→48.552 Å / Num. obs: 92339 / % possible obs: 99.39 % / Redundancy: 1.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.04858 / Rpim(I) all: 0.04858 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.9→1.968 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.3653 / Mean I/σ(I) obs: 2.52 / Num. unique obs: 9196 / CC1/2: 0.779 / Rpim(I) all: 0.3653 / % possible all: 99.38 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2o1x Resolution: 1.9→48.552 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / Cross valid method: FREE R-VALUE / ESU R: 0.116 / ESU R Free: 0.113 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: 22.378 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→48.552 Å
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Refine LS restraints |
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LS refinement shell |
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