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Open data
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Basic information
Entry | Database: PDB / ID: 1onp | ||||||
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Title | IspC complex with Mn2+ and fosmidomycin | ||||||
![]() | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | ||||||
![]() | OXIDOREDUCTASE / isoprenoid biosynthesis / mevalonate-independent pathway / IspC | ||||||
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 | ![]() ![]() | ||||||
![]() | Steinbacher, S. / Kaiser, J. / Eisenreich, W. / Huber, R. / Bacher, A. / Rohdich, F. | ||||||
![]() | ![]() Title: Structural basis of fosmidomycin action revealed by the complex with 2-C-methyl-D-erythritol 4-phosphate synthase (IspC). Implications for the catalytic mechanism and anti-malaria drug development. Authors: Steinbacher, S. / Kaiser, J. / Eisenreich, W. / Huber, R. / Bacher, A. / Rohdich, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 165.4 KB | Display | ![]() |
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PDB format | ![]() | 130.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 397.2 KB | Display | ![]() |
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Full document | ![]() | 437.2 KB | Display | |
Data in XML | ![]() | 22.5 KB | Display | |
Data in CIF | ![]() | 33.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1onnC ![]() 1onoC ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 43431.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P45568, 1-deoxy-D-xylulose-5-phosphate reductoisomerase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.11 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8 Details: PEG 4000, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 21 ℃ / pH: 8 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 12, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.548 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. all: 34930 / Num. obs: 34930 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.083 |
Reflection shell | Resolution: 2.5→2.59 Å / Rmerge(I) obs: 0.417 / % possible all: 98.5 |
Reflection | *PLUS Lowest resolution: 20 Å |
Reflection shell | *PLUS Highest resolution: 2.5 Å / % possible obs: 98.5 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1K5H Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å / Num. reflection obs: 33163 / % reflection Rfree: 4.9 % / Rfactor Rfree: 0.33 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |