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Yorodumi- PDB-5cc9: L28F E.coli dihydrofolate reductase complexed with 5,10-dideazate... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cc9 | ||||||
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Title | L28F E.coli dihydrofolate reductase complexed with 5,10-dideazatetrahydrofolate and oxidized nicotinamide adenine dinucleotide phosphate | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / Folate metabolism | ||||||
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 (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.199 Å | ||||||
Authors | Oyen, D. / Wright, P.E. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2015 Title: Cofactor-Mediated Conformational Dynamics Promote Product Release From Escherichia coli Dihydrofolate Reductase via an Allosteric Pathway. Authors: Oyen, D. / Fenwick, R.B. / Stanfield, R.L. / Dyson, H.J. / 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 | 5cc9.cif.gz | 126.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cc9.ent.gz | 99.7 KB | Display | PDB format |
PDBx/mmJSON format | 5cc9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cc9_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5cc9_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5cc9_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 5cc9_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cc/5cc9 ftp://data.pdbj.org/pub/pdb/validation_reports/cc/5cc9 | HTTPS FTP |
-Related structure data
Related structure data | 5cccC 1rx6S 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: 18053.357 Da / Num. of mol.: 1 / Mutation: L28F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: folA / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): dnaY References: UniProt: P0ABQ5, UniProt: P0ABQ4*PLUS, dihydrofolate reductase |
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#2: Chemical | ChemComp-NAP / |
#3: Chemical | ChemComp-DDF / |
#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: 2.19 Å3/Da / Density % sol: 44.37 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M tris(hydroxymethyl)aminomethane, 20% w/v PEG3350, 0.2M calcium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 1.2→46.96 Å / Num. all: 50682 / Num. obs: 50682 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.2 % / Biso Wilson estimate: 14.3 Å2 / Rsym value: 0.046 / Net I/σ(I): 43.8 |
Reflection shell | Resolution: 1.2→1.22 Å / Redundancy: 12.2 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RX6 Resolution: 1.199→46.959 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.85 / 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: 1.199→46.959 Å
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Refine LS restraints |
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LS refinement shell |
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