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Yorodumi- PDB-7f3b: cocrystallization of Escherichia coli dihydrofolate reductase (DH... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7f3b | |||||||||
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Title | cocrystallization of Escherichia coli dihydrofolate reductase (DHFR) and its pyrrolo[3,2-f]quinazoline inhibitor. | |||||||||
Components | Dihydrofolate reductase | |||||||||
Keywords | ANTIBIOTIC / folate pathway / dihydrofolate reductase / catalyze the reduction of dihydrofolate to tetrahydrofolate | |||||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å | |||||||||
Authors | Wang, H. / You, X.F. / Yang, X.Y. / Li, Y. / Hong, W. | |||||||||
Funding support | China, 2items
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Citation | Journal: Eur.J.Med.Chem. / Year: 2022 Title: The discovery of 1, 3-diamino-7H-pyrrol[3, 2-f]quinazoline compounds as potent antimicrobial antifolates. Authors: Li, Y. / Ouyang, Y. / Wu, H. / Wang, P. / Huang, Y. / Li, X. / Chen, H. / Sun, Y. / Hu, X. / Wang, X. / Li, G. / Lu, Y. / Li, C. / Lu, X. / Pang, J. / Nie, T. / Sang, X. / Dong, L. / Dong, W. ...Authors: Li, Y. / Ouyang, Y. / Wu, H. / Wang, P. / Huang, Y. / Li, X. / Chen, H. / Sun, Y. / Hu, X. / Wang, X. / Li, G. / Lu, Y. / Li, C. / Lu, X. / Pang, J. / Nie, T. / Sang, X. / Dong, L. / Dong, W. / Jiang, J. / Paterson, I.C. / Yang, X. / Hong, W. / Wang, H. / You, X. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7f3b.cif.gz | 94.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7f3b.ent.gz | 59.6 KB | Display | PDB format |
PDBx/mmJSON format | 7f3b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7f3b_validation.pdf.gz | 741.1 KB | Display | wwPDB validaton report |
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Full document | 7f3b_full_validation.pdf.gz | 744.2 KB | Display | |
Data in XML | 7f3b_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 7f3b_validation.cif.gz | 10.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/7f3b ftp://data.pdbj.org/pub/pdb/validation_reports/f3/7f3b | HTTPS FTP |
-Related structure data
Related structure data | 1ddsS 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: 18848.223 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SF file contains Friedel pairs. Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: folA, tmrA, b0048, JW0047 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P0ABQ4, dihydrofolate reductase | ||
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#2: Chemical | ChemComp-D4C / | ||
#3: Chemical | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.37 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 3.5 Details: 12% (wt/vol) PEG 20000, 5% (vol/vol) 2-propanol, and 0,1M sodium citrate, pH3.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97935 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 8, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97935 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 8606 / % possible obs: 99.5 % / Redundancy: 19.3 % / Biso Wilson estimate: 50.85 Å2 / CC1/2: 0.958 / Rpim(I) all: 0.066 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.8→2.9 Å / Num. unique obs: 576 / CC1/2: 0.966 / Rpim(I) all: 0.276 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DDS Resolution: 2.81→49.39 Å / SU ML: 0.2278 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.0799 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: 53.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.81→49.39 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -18.3116879938 Å / Origin y: 21.7002646276 Å / Origin z: -2.49716672126 Å
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Refinement TLS group | Selection details: all |