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- PDB-3anm: Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomer... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3anm | ||||||
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Title | Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) complexed with 5-phenylpyridin-2-ylmethylphosphonic acid | ||||||
![]() | 1-deoxy-D-xylulose 5-phosphate reductoisomerase | ||||||
![]() | OXIDOREDUCTASE / reductoisomerase / NADPH binding | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Endo, K. / Kato, M. / Deng, L. / Song, Y. / Yajima, S. | ||||||
![]() | ![]() Title: Structures of 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase/Lipophilic Phosphonate Complexes Authors: Deng, L. / Endo, K. / Kato, M. / Cheng, G. / Yajima, S. / Song, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 173.4 KB | Display | ![]() |
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PDB format | ![]() | 135.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3anlC ![]() 3annC ![]() 2eghS S: Starting model for refinement C: citing same article ( |
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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: 45746.375 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: 2.57 Å3/Da / Density % sol: 52.1 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1M sodium citrate, 0.8M sodium malonate, 0.3M potassium sodium (+) tartrate, 3mM NADPH, 5mM MgCl2, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 13, 2010 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 64644 / Num. obs: 64256 / % possible obs: 99.4 % / Observed criterion σ(F): 0.0001 / Observed criterion σ(I): 0.0001 / Redundancy: 3.7 % |
Reflection shell | Resolution: 2→2.03 Å / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2EGH Resolution: 2→29.2 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.274 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.593 Å2
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Refinement step | Cycle: LAST / Resolution: 2→29.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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