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Yorodumi- PDB-4qle: Crystal structure of I14A DHFR mutant complexed with folate and NADP+ -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qle | ||||||
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Title | Crystal structure of I14A DHFR mutant complexed with folate and NADP+ | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE / dihydrofolate-reductase like fold/Alpha and beta proteins (a/b) / oxidoreductase activity / NADP(H) binding | ||||||
Function / homology | Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 3-Layer(aba) Sandwich / Alpha Beta / FOLIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / : Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Stojkovic, V. / Gakhar, L. / Kohen, A. | ||||||
Citation | Journal: J.Phys.Chem.B / Year: 2015 Title: Free energy simulations of active-site mutants of dihydrofolate reductase. Authors: Doron, D. / Stojkovic, V. / Gakhar, L. / Vardi-Kilshtain, A. / Kohen, A. / Major, D.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qle.cif.gz | 166.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qle.ent.gz | 131.9 KB | Display | PDB format |
PDBx/mmJSON format | 4qle.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qle_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4qle_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4qle_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 4qle_validation.cif.gz | 29 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ql/4qle ftp://data.pdbj.org/pub/pdb/validation_reports/ql/4qle | HTTPS FTP |
-Related structure data
Related structure data | 4qlfC 4qlgC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17977.260 Da / Num. of mol.: 2 / Fragment: DIHYDROFOLATE REDUCTASE / Mutation: I14A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: folA, BN896_0046 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: U6N356, dihydrofolate reductase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 42.71 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2 M Lithium acetate, 20% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.855 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Jun 9, 2011 |
Radiation | Monochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.855 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→73.88 Å / Num. all: 66630 / Num. obs: 66630 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 21.22 |
Reflection shell | Resolution: 1.35→1.42 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RX2 Resolution: 1.35→30.48 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.479 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.054 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.511 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→30.48 Å
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Refine LS restraints |
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