+Open data
-Basic information
Entry | Database: PDB / ID: 7fq6 | |||||||||||||||
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Title | DHFR:NADP+:FOL complex at 310 K (multi-crystal) | |||||||||||||||
Components | Dihydrofolate reductase | |||||||||||||||
Keywords | OXIDOREDUCTASE / Dihydrofolate Reductase | |||||||||||||||
Function / homology | Function and homology information 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 | Escherichia coli K-12 (bacteria) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.29 Å | |||||||||||||||
Authors | Greisman, J.B. / Dalton, K.M. / Brookner, D.E. / Hekstra, D.R. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2024 Title: Perturbative diffraction methods resolve a conformational switch that facilitates a two-step enzymatic mechanism. Authors: Greisman, J.B. / Dalton, K.M. / Brookner, D.E. / Klureza, M.A. / Sheehan, C.J. / Kim, I.S. / Henning, R.W. / Russi, S. / Hekstra, D.R. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fq6.cif.gz | 134.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fq6.ent.gz | 109.4 KB | Display | PDB format |
PDBx/mmJSON format | 7fq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/7fq6 ftp://data.pdbj.org/pub/pdb/validation_reports/fq/7fq6 | HTTPS FTP |
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-Group deposition
ID | G_1002249 (4 entries) |
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Title | DHFR:NADP+:FOL complex at 310 K |
Type | undefined |
Description | DHFR:NADP+:FOL complex at 310 K |
-Related structure data
Related structure data | 7lvcS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18051.338 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: folA, tmrA, b0048, JW0047 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABQ4, dihydrofolate reductase | ||||
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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: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.21 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 20 mM imadazole (pH 5.4-5.8), 16-21% PEG 400, 125 mM MnCl2 PH range: 5.4 - 5.8 |
-Data collection
Diffraction | Mean temperature: 310 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.826533 / Wavelength: 0.826533 Å |
Detector | Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Nov 20, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.826533 Å / Relative weight: 1 |
Reflection | Resolution: 1.29→99.25 Å / Num. obs: 74931 / % possible obs: 99.8 % / Redundancy: 82.2 % / Biso Wilson estimate: 18.97 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.884 / Rpim(I) all: 0.098 / Net I/σ(I): 31.6 |
Reflection shell | Resolution: 1.29→1.31 Å / % possible obs: 94 % / Redundancy: 84.7 % / Rmerge(I) obs: 7.79 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 3378 / CC1/2: 0.326 / Rpim(I) all: 0.839 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 7LVC Resolution: 1.29→26.72 Å / SU ML: 0.2051 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.5341 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 25.21 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.29→26.72 Å
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Refine LS restraints |
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LS refinement shell |
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