+Open data
-Basic information
Entry | Database: PDB / ID: 5uio | ||||||
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Title | structure of DHFR with bound DAP, p-ABG and NADP | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / DHFR / NADP / 2 / 4 diaminopyridine / N-(4aminobenzoyl)-L-glutamate | ||||||
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: 1.929 Å | ||||||
Authors | Pedersen, L.C. / London, R.E. | ||||||
Citation | Journal: Biochemistry / Year: 2017 Title: A Structural Basis for Biguanide Activity. Authors: Gabel, S.A. / Duff, M.R. / Pedersen, L.C. / DeRose, E.F. / Krahn, J.M. / Howell, E.E. / London, R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5uio.cif.gz | 192.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uio.ent.gz | 154.3 KB | Display | PDB format |
PDBx/mmJSON format | 5uio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/5uio ftp://data.pdbj.org/pub/pdb/validation_reports/ui/5uio | HTTPS FTP |
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-Related structure data
Related structure data | 5uihC 5uiiC 5uipC 1ra3S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 1 types, 5 molecules ABCDE
#1: Protein | Mass: 19207.625 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: folA / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABQ4, dihydrofolate reductase |
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-Non-polymers , 6 types, 635 molecules
#2: Chemical | ChemComp-LG3 / #3: Chemical | ChemComp-8DM / #4: Chemical | ChemComp-NAP / #5: Chemical | ChemComp-BME / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 2mM NADP,10mM DAP,50mM p-ABP,0.2M Magnesium Formate,20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→50 Å / Num. obs: 72439 / % possible obs: 100 % / Redundancy: 7.9 % / Rsym value: 0.058 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.93→1.96 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3616 / Rsym value: 0.475 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RA3 Resolution: 1.929→35.446 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.929→35.446 Å
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Refine LS restraints |
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LS refinement shell |
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