+Open data
-Basic information
Entry | Database: PDB / ID: 6cyv | ||||||
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Title | E. coli DHFR ternary complex with NADP and dihydrofolate | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / DHFR / dihydrofolate reductase / dihydrofolate / NADP / ternary complex | ||||||
Function / homology | Function and homology information dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli O6:H1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 Å | ||||||
Authors | Cao, H. / Rodrigues, J. / Benach, J. / Frommelt, A. / Morisco, L. / Koss, J. / Shakhnovich, E. / Skolnick, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Commun Biol / Year: 2018 Title: The crystal structure of a tetrahydrofolate-bound dihydrofolate reductase reveals the origin of slow product release. Authors: Cao, H. / Gao, M. / Zhou, H. / Skolnick, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cyv.cif.gz | 83.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cyv.ent.gz | 60.6 KB | Display | PDB format |
PDBx/mmJSON format | 6cyv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/6cyv ftp://data.pdbj.org/pub/pdb/validation_reports/cy/6cyv | HTTPS FTP |
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-Related structure data
Related structure data | 6cqaC 6cw7C 6cxkC 7dfrS 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
#1: Protein | Mass: 18848.223 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) (bacteria) Strain: CFT073 / ATCC 700928 / UPEC / Gene: folA, c0058 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABQ5, dihydrofolate reductase |
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#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-DHF / |
#4: 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: 2.16 Å3/Da / Density % sol: 42.94 % / Description: long thin plate |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1:1 v/v mixing ratio of 30 mg/ml of purified E. coli DHFR in 20mM Tris pH 8, 1mM DTT and reservoir solution containing 0.1M Imidazole pH8, 50mM Calcium acetate and 20% PEG 6000. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Feb 28, 2018 / Details: Diamond(111) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Kohzu HLD-4 Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.09→32.872 Å / Num. obs: 54649 / % possible obs: 79.6 % / Redundancy: 6.246 % / Biso Wilson estimate: 16.21 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.103 / Χ2: 1.037 / Net I/σ(I): 9.32 / Num. measured all: 341343 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7dfr Resolution: 1.3→32.872 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.96
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.51 Å2 / Biso mean: 23.84 Å2 / Biso min: 10.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.3→32.872 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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