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Open data
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Basic information
Entry | Database: PDB / ID: 1q0l | ||||||
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Title | Crystal structure of DXR in complex with fosmidomycin | ||||||
![]() | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | ||||||
![]() | OXIDOREDUCTASE | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Mac Sweeney, A. / Lange, R. / D'Arcy, A. / Douangamath, A. / Surivet, J.-P. / Oefner, C. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90.8 KB | Display | ![]() |
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PDB format | ![]() | 67.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 790.5 KB | Display | ![]() |
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Full document | ![]() | 794.7 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 24.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1q0hC ![]() 1q0qC ![]() 1k5hS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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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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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) |
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Components
#1: Protein | Mass: 44404.879 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P45568, 1-deoxy-D-xylulose-5-phosphate reductoisomerase |
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#2: Chemical | ChemComp-FOM / |
#3: Chemical | ChemComp-NDP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.53 Å3/Da / Density % sol: 65.2 % |
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Crystal grow | Temperature: 298 K / Method: microbatch under oil / pH: 6.5 Details: 25% P3350, 200mM Li2SO4, 100mM Bis-Tris pH 6.5, Microbatch under oil, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 28, 2002 / 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: 2.65→20 Å / Num. all: 18739 / Num. obs: 18451 / % possible obs: 99.2 % / Observed criterion σ(F): 6 / Observed criterion σ(I): 6 / Redundancy: 6.8 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.65→2.82 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.98 / % possible all: 95.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1K5H (NADPH binding domain) Resolution: 2.65→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 6 / σ(I): 6 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 25.5 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→20 Å
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Refine LS restraints |
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