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Yorodumi- PDB-8a9c: Structure of truncated 1-deoxy-D-xylulose 5-phosphate synthase (D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a9c | ||||||
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Title | Structure of truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Klebsiella pneumoniae in complex with cofactor TPP | ||||||
Components | 1-deoxy-D-xylulose-5-phosphate synthase | ||||||
Keywords | TRANSFERASE / Primary metabolism / synthase / complex | ||||||
Function / homology | Function and homology information 1-deoxy-D-xylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase activity / 1-deoxy-D-xylulose 5-phosphate biosynthetic process / thiamine biosynthetic process / terpenoid biosynthetic process / thiamine pyrophosphate binding / magnesium ion binding Similarity search - Function | ||||||
Biological species | Klebsiella pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Adam, S. / Hirsch, A. | ||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published Title: Structure of truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Klebsiella pneumoniae in complex with cofactor TPP Authors: Adam, S. / Hirsch, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a9c.cif.gz | 428.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a9c.ent.gz | 347.8 KB | Display | PDB format |
PDBx/mmJSON format | 8a9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/8a9c ftp://data.pdbj.org/pub/pdb/validation_reports/a9/8a9c | HTTPS FTP |
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-Related structure data
Related structure data | 2o1sS 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
#1: Protein | Mass: 63254.125 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) Gene: dxs_3, dxs, dxs_1, BN49_1346, FXN67_12755, GJJ18_13560, GJJ26_020415, NCTC11679_04435, NCTC13465_06397, NCTC3279_00555, NCTC5047_01280, NCTC5052_00313, NCTC9140_02292, NCTC9645_03343, NCTC9661_ ...Gene: dxs_3, dxs, dxs_1, BN49_1346, FXN67_12755, GJJ18_13560, GJJ26_020415, NCTC11679_04435, NCTC13465_06397, NCTC3279_00555, NCTC5047_01280, NCTC5052_00313, NCTC9140_02292, NCTC9645_03343, NCTC9661_05006, SAMEA3649733_02709, SAMEA4364603_02966, dxs_3, dxs, dxs_1, dxs_2, BN49_1346, DRB11_07540, FXN67_12755, NCTC11679_04435, NCTC13465_06397, NCTC3279_00555, NCTC5047_01280, NCTC5052_00313, NCTC9140_02292, NCTC9645_03343, NCTC9661_05006, SAMEA3512100_02923, SAMEA3649733_02709, SAMEA4364603_02966 Production host: Escherichia coli (E. coli) References: UniProt: A0A0S3F934, 1-deoxy-D-xylulose-5-phosphate synthase #2: Chemical | ChemComp-TPP / | #3: Chemical | ChemComp-MG / | #4: 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: 2.23 Å3/Da / Density % sol: 44.85 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: PEG 3000, HEPES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 19, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→43.37 Å / Num. obs: 100675 / % possible obs: 97.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 25.3600941464 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.8→1.9 Å / Rmerge(I) obs: 0.561 / Num. unique obs: 14606 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2o1s Resolution: 1.8→43.37 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→43.37 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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