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Yorodumi- PDB-1q0h: Crystal structure of selenomethionine-labelled DXR in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q0h | ||||||
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Title | Crystal structure of selenomethionine-labelled DXR in complex with fosmidomycin | ||||||
Components | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information Dxr protein complex / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway involved in terpenoid biosynthetic process / 1-deoxy-D-xylulose-5-phosphate reductoisomerase / 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / NADPH binding / manganese ion binding / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Mac Sweeney, A. / Lange, R. / D'Arcy, A. / Douangamath, A. / Surivet, J.-P. / Oefner, C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: The crystal structure of E.coli 1-deoxy-D-xylulose-5-phosphate reductoisomerase in a ternary complex with the antimalarial compound fosmidomycin and NADPH reveals a tight-binding closed enzyme conformation. Authors: Mac Sweeney, A. / Lange, R. / Fernandes, R.P. / Schulz, H. / Dale, G.E. / Douangamath, A. / Proteau, P.J. / Oefner, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q0h.cif.gz | 99 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q0h.ent.gz | 74.4 KB | Display | PDB format |
PDBx/mmJSON format | 1q0h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q0/1q0h ftp://data.pdbj.org/pub/pdb/validation_reports/q0/1q0h | HTTPS FTP |
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-Related structure data
Related structure data | 1q0lC 1q0qC 1k5hS 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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Details | The second molecule of the biological homodimer is generated by the two-fold axis. Operation x, y, z to y, x, 1-z (non-orthogonal coordinate system) |
-Components
#1: Protein | Mass: 45295.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: DXR / Plasmid: pDS-6hisNdeI / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P45568, 1-deoxy-D-xylulose-5-phosphate reductoisomerase |
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#2: Chemical | ChemComp-FOM / |
#3: Chemical | ChemComp-NDP / |
#4: Chemical | ChemComp-CIT / |
#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: 3.44 Å3/Da / Density % sol: 64.26 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 2.6M NaCl, 0.1M Acetate-HCl pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 2003 / Details: Osmic mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. all: 32094 / Num. obs: 31221 / % possible obs: 97.1 % / Observed criterion σ(F): 6 / Observed criterion σ(I): 6 / Redundancy: 3.8 % / Biso Wilson estimate: 0.23 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 7.64 |
Reflection shell | Resolution: 2.2→2.34 Å / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 1.97 / % possible all: 94.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1K5H (NADPH binding domain) Resolution: 2.2→17.62 Å / Isotropic thermal model: isotropic / σ(F): 6 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 23.8 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→17.62 Å
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Refine LS restraints |
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