+Open data
-Basic information
Entry | Database: PDB / ID: 4x5j | ||||||
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Title | ecDHFR complexed with folate and NADP+ at 750 MPa | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE | ||||||
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 K12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å | ||||||
Authors | Yamada, H. / Watanabe, N. / Nagae, T. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: High-pressure protein crystal structure analysis of Escherichia coli dihydrofolate reductase complexed with folate and NADP. Authors: Nagae, T. / Yamada, H. / Watanabe, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4x5j.cif.gz | 52.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x5j.ent.gz | 35.2 KB | Display | PDB format |
PDBx/mmJSON format | 4x5j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/4x5j ftp://data.pdbj.org/pub/pdb/validation_reports/x5/4x5j | HTTPS FTP |
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-Related structure data
Related structure data | 4x5fC 4x5gC 4x5hC 4x5iC 5z6fC 5z6jC 5z6kC 5z6lC 5z6mC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18301.619 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K12 (bacteria) / Gene: folA, tmrA, b0048, JW0047 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABQ4, dihydrofolate reductase |
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#2: Chemical | ChemComp-FOL / |
#3: Chemical | ChemComp-NAP / |
#4: Chemical | ChemComp-BME / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.03 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 6000, imidazole, calcium chloride |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.71 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jan 20, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.71 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 13475 / % possible obs: 98.3 % / Redundancy: 5.1 % / Net I/σ(I): 16.7 |
-Processing
Software |
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Refinement | Resolution: 1.85→36.54 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.88 / SU B: 4.611 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 20.701 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→36.54 Å
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Refine LS restraints |
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