+Open data
-Basic information
Entry | Database: PDB / ID: 4nx6 | ||||||
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Title | single room temperature model of DHFR | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / folate metabolism | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Fenwick, R.B. / van den Bedem, H. / Fraser, J.S. / Wright, P.E. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR. Authors: Fenwick, R.B. / van den Bedem, H. / Fraser, J.S. / Wright, P.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nx6.cif.gz | 114 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nx6.ent.gz | 87.7 KB | Display | PDB format |
PDBx/mmJSON format | 4nx6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nx/4nx6 ftp://data.pdbj.org/pub/pdb/validation_reports/nx/4nx6 | HTTPS FTP |
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-Related structure data
Related structure data | 4nx7C 1rx2S 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18019.340 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: folA, tmrA / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABQ4, dihydrofolate reductase |
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-Non-polymers , 5 types, 172 molecules
#2: Chemical | ChemComp-FOL / |
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#3: Chemical | ChemComp-BME / |
#4: Chemical | ChemComp-NAP / |
#5: Chemical | ChemComp-MN / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100MM HEPES PH 7.5, 21% PEG8000, 200MM MGCL2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.953724 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 11, 2011 |
Radiation | Monochromator: KOHZU DUAL DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953724 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→50 Å / Num. all: 31891 / Num. obs: 31891 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.35→1.4 Å / % possible all: 48.7 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: dev_1328) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1RX2 Resolution: 1.35→41.344 Å / SU ML: 0.14 / σ(F): 1.34 / Phase error: 18.95 / 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: 1.35→41.344 Å
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Refine LS restraints |
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LS refinement shell |
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