+Open data
-Basic information
Entry | Database: PDB / ID: 5uip | ||||||
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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: 1.9 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 | 5uip.cif.gz | 93.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5uip.ent.gz | 68 KB | Display | PDB format |
PDBx/mmJSON format | 5uip.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ui/5uip ftp://data.pdbj.org/pub/pdb/validation_reports/ui/5uip | HTTPS FTP |
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-Related structure data
Related structure data | 5uihC 5uiiC 5uioC 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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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 18157.338 Da / Num. of mol.: 2 / Mutation: C152S 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 , 5 types, 396 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: 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: 2.18 Å3/Da / Density % sol: 43.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 2mM NADP,10mM 2,4 diaminopyridine,50mM N-(4aminobenzoyl)-L-glutamate |
-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 92 / Detector: CCD / Date: Jul 8, 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: 1.9→50 Å / Num. obs: 23632 / % possible obs: 97.5 % / Redundancy: 3.4 % / Rsym value: 0.05 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 7.8 / Rsym value: 0.127 / % possible all: 81.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ra3 Resolution: 1.9→21.809 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 19.31
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→21.809 Å
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Refine LS restraints |
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LS refinement shell |
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