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Yorodumi- PDB-1juv: Crystal structure analysis of Dihydrofolate reductase from Bacter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1juv | ||||||
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Title | Crystal structure analysis of Dihydrofolate reductase from Bacteriophage T4 | ||||||
Components | DIHYDROFOLATE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / complexed with NADPH | ||||||
Function / homology | Function and homology information response to methotrexate / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / response to antibiotic Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.7 Å | ||||||
Authors | Moon, J.H. / Oh, Y.K. / Suh, S.W. | ||||||
Citation | Journal: To be Published Title: Crystal structure analysis of Dihydrofolate reductase from Bacteriophage T4 Authors: Moon, J.H. / Oh, Y.K. / Lee, J.Y. / Suh, S.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1juv.cif.gz | 55.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1juv.ent.gz | 40 KB | Display | PDB format |
PDBx/mmJSON format | 1juv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/1juv ftp://data.pdbj.org/pub/pdb/validation_reports/ju/1juv | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21737.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: frd / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: P04382, dihydrofolate reductase |
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#2: Chemical | ChemComp-NDP / |
#3: 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: 2.44 Å3/Da / Density % sol: 49.29 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.1 Details: NaCl, (NH4)2HPO4 , pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Jan 1, 2000 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 26714 / Num. obs: 26714 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.068 |
Reflection shell | Resolution: 1.7→1.76 Å / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.7→43.57 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 922023.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 53.7805 Å2 / ksol: 0.398346 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→43.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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