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- PDB-7nae: Crystal structure of Escherichia coli dihydrofolate reductase in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7nae | ||||||
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Title | Crystal structure of Escherichia coli dihydrofolate reductase in complex with TRIMETHOPRIM | ||||||
![]() | Dihydrofolate reductase | ||||||
![]() | OXIDOREDUCTASE / dihydrofolate reductase | ||||||
Function / homology | ![]() methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process ...methotrexate binding / dihydrofolic acid binding / response to methotrexate / NADP+ binding / folic acid binding / dihydrofolate metabolic process / glycine biosynthetic 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 | ![]() ![]() ![]() | ||||||
![]() | Estrada, A. / Wright, D. / Krucinska, J. / Erlandsen, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure-guided functional studies of plasmid-encoded dihydrofolate reductases reveal a common mechanism of trimethoprim resistance in Gram-negative pathogens. Authors: Krucinska, J. / Lombardo, M.N. / Erlandsen, H. / Estrada, A. / Si, D. / Viswanathan, K. / Wright, D.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.8 KB | Display | ![]() |
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PDB format | ![]() | 33.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 777 KB | Display | ![]() |
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Full document | ![]() | 779.1 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 11.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7mqpC ![]() 7mylC ![]() 7mymSC ![]() 7r6gC ![]() 7rebC ![]() 7regC ![]() 7rgjC ![]() 7rgkC ![]() 7rgoC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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 on special symmetry positions |
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Components
#1: Protein | Mass: 19366.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: folA, tmrA, b0048, JW0047 / Production host: ![]() ![]() | ||||
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#2: Chemical | ChemComp-TOP / | ||||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.44 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop Details: 18% to 20% PEG4K or 8K, 0.2M Ammonium Sulfate and 2mM DTT |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Aug 21, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→56.83 Å / Num. obs: 11767 / % possible obs: 96.1 % / Redundancy: 1.8 % / CC1/2: 1 / Rmerge(I) obs: 0.014 / Rpim(I) all: 0.014 / Rrim(I) all: 0.02 / Net I/σ(I): 30.2 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 5 / Num. unique obs: 1154 / CC1/2: 0.964 / Rpim(I) all: 0.162 / Rrim(I) all: 0.229 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7MYM Resolution: 2.35→56.83 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.895 / SU B: 6.409 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.238 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 159.56 Å2 / Biso mean: 57.544 Å2 / Biso min: 36.3 Å2
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Refinement step | Cycle: final / Resolution: 2.35→56.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.411 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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