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Yorodumi- PDB-8vz4: L54G Mutant of E. coli Dihydrofolate Reductase Complexed with Nic... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vz4 | |||||||||
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Title | L54G Mutant of E. coli Dihydrofolate Reductase Complexed with Nicotinamide Adenine Dinucleotide Phosphate (oxidized form) | |||||||||
Components | Dihydrofolate reductase | |||||||||
Keywords | OXIDOREDUCTASE / L54G / NADP+ / DHFR | |||||||||
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: 1.25 Å | |||||||||
Authors | Fried, S.D.E. / Boxer, S.G. | |||||||||
Funding support | United States, 2items
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Citation | Journal: To Be Published Title: Role of Electrostatics in Hydride Transfer by Dihydrofolate Reductase Authors: Fried, S.D.E. / Mukherjee, S. / Mao, Y. / Boxer, S.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vz4.cif.gz | 168.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vz4.ent.gz | 133.9 KB | Display | PDB format |
PDBx/mmJSON format | 8vz4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vz/8vz4 ftp://data.pdbj.org/pub/pdb/validation_reports/vz/8vz4 | HTTPS FTP |
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-Related structure data
Related structure data | 8ucxC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 17963.234 Da / Num. of mol.: 2 / Mutation: L54G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: folA, tmrA, b0048, JW0047 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABQ4, dihydrofolate reductase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.92 % / Description: Rods |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 6000, calcium chloride, Tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 21, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→37.64 Å / Num. obs: 83315 / % possible obs: 98.5 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.038 / Rrim(I) all: 0.144 / Χ2: 0.87 / Net I/σ(I): 10.1 / Num. measured all: 1134224 |
Reflection shell | Resolution: 1.25→1.27 Å / % possible obs: 91.4 % / Redundancy: 11.2 % / Rmerge(I) obs: 3.157 / Num. measured all: 42599 / Num. unique obs: 3797 / CC1/2: 0.762 / Rpim(I) all: 0.955 / Rrim(I) all: 3.305 / Χ2: 0.8 / Net I/σ(I) obs: 1.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→37.64 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.84 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→37.64 Å
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Refine LS restraints |
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LS refinement shell |
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