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- PDB-7d4l: X-ray crystal Structure of E.coli Dihydrofolate Reductase complex... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7d4l | |||||||||
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Title | X-ray crystal Structure of E.coli Dihydrofolate Reductase complexed with folate and NADP+ at pH7.0 | |||||||||
![]() | Dihydrofolate reductase | |||||||||
![]() | OXIDOREDUCTASE / dihydrofolate / reductase / alpha-beta sandiwitch / NADPH | |||||||||
Function / homology | ![]() methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding ...methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to xenobiotic stimulus / response to antibiotic / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
Model details | X-ray diffraction | |||||||||
![]() | Wan, Q. / Dealwis, C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Capturing the Catalytic Proton of Dihydrofolate Reductase: Implications for General Acid-Base Catalysis Authors: Wan, Q. / Bennett, B.C. / Wymore, T. / Li, Z. / Wilson, M.A. / Brooks III, C.L. / Langan, P. / Kovalevsky, A. / Dealwis, C.G. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 51.9 KB | Display | ![]() |
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PDB format | ![]() | 34.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7d3zC ![]() 7d49C ![]() 7d4xC ![]() 7d6gC ![]() 1rx2S 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 18020.326 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: folA, tmrA, b0048, JW0047 / Plasmid: pET-sumo / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-FOL / |
#3: Chemical | ChemComp-NAP / |
#4: Chemical | ChemComp-MN / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.75 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 40mg/mL DHFR-folate-NADP+ complex, 12% (v/v) PEG 400, 100mM MnCl2, 20mM imidazole, pH7.0 |
-Data collection
Diffraction | Mean temperature: 291 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 10, 2014 / Details: VariMax |
Radiation | Monochromator: CHOPPER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 20795 / % possible obs: 97.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 18.08 Å2 / Rmerge(I) obs: 0.097 / Χ2: 1.081 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 4 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 2.97 / Num. unique obs: 1017 / Χ2: 0.98 / % possible all: 94 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1rx2 Resolution: 1.6→27.41 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.54 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.28 Å2 / Biso mean: 21.0129 Å2 / Biso min: 9.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→27.41 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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