[English] 日本語
Yorodumi- PDB-7d4l: X-ray crystal Structure of E.coli Dihydrofolate Reductase complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7d4l | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | X-ray crystal Structure of E.coli Dihydrofolate Reductase complexed with folate and NADP+ at pH7.0 | |||||||||
Components | Dihydrofolate reductase | |||||||||
Keywords | OXIDOREDUCTASE / dihydrofolate / reductase / alpha-beta sandiwitch / NADPH | |||||||||
Function / homology | Function and homology information methotrexate binding / dihydrofolic acid binding / response to methotrexate / dihydrofolate metabolic process / NADP+ binding / folic acid binding / folic acid metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity ...methotrexate binding / dihydrofolic acid binding / response to methotrexate / dihydrofolate metabolic process / NADP+ binding / folic acid binding / folic acid metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / NADPH binding / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to xenobiotic stimulus / response to antibiotic / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Model details | X-ray diffraction | |||||||||
Authors | Wan, Q. / Dealwis, C. | |||||||||
Funding support | China, 2items
| |||||||||
Citation | Journal: Acs Catalysis / Year: 2021 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7d4l.cif.gz | 51.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7d4l.ent.gz | 34.3 KB | Display | PDB format |
PDBx/mmJSON format | 7d4l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/7d4l ftp://data.pdbj.org/pub/pdb/validation_reports/d4/7d4l | HTTPS FTP |
---|
-Related structure data
Related structure data | 7d3zC 7d49C 7d4xC 7d6gC 1rx2S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18020.326 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Gene: folA, tmrA, b0048, JW0047 / Plasmid: pET-sumo / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABQ4, dihydrofolate reductase |
---|---|
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.75 % |
---|---|
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 |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|