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Yorodumi- PDB-7mqp: E. coli dihydrofolate reductase complexed with 4'-chloro-3'-(4-(2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7mqp | ||||||
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Title | E. coli dihydrofolate reductase complexed with 4'-chloro-3'-(4-(2,4-diamino-6-ethylpyrimidin-5-yl)but-3-yn-2-yl)-[1,1'-biphenyl]-4-carboxamide (UCP1228) | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / Inhibitor / antifolate / DHFR | ||||||
Function / homology | Function and homology information dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Lombardo, M.N. / Wright, D.L. | ||||||
Funding support | 1items
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Citation | Journal: Commun Biol / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7mqp.cif.gz | 53 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7mqp.ent.gz | 35.7 KB | Display | PDB format |
PDBx/mmJSON format | 7mqp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/7mqp ftp://data.pdbj.org/pub/pdb/validation_reports/mq/7mqp | HTTPS FTP |
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-Related structure data
Related structure data | 7mylC 7mymC 7naeC 7r6gC 7rebC 7regC 7rgjC 7rgkC 7rgoC 1rf7S S: Starting model for refinement C: citing same article (ref.) |
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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: 18262.600 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: folA, folA_1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3TR70, dihydrofolate reductase | ||||
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#2: Chemical | ChemComp-ZM4 / | ||||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | 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: 3.76 Å3/Da / Density % sol: 67.25 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: 0.3-0.35 M lithium sulfate, 15-19% PEG 6,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 16, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→57.81 Å / Num. obs: 17232 / % possible obs: 99.72 % / Redundancy: 1.2 % / CC1/2: 1 / CC star: 1 / Net I/σ(I): 21.82 |
Reflection shell | Resolution: 2.102→2.177 Å / Redundancy: 1.1 % / Mean I/σ(I) obs: 3.73 / Num. unique obs: 1663 / CC1/2: 1 / CC star: 1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RF7 Resolution: 2.1→57.81 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.225 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.147 / 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: 163.31 Å2 / Biso mean: 65.274 Å2 / Biso min: 42.48 Å2
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Refinement step | Cycle: final / Resolution: 2.1→57.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.102→2.156 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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