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Yorodumi- PDB-4qlg: Crystal structure of I14V DHFR mutant complexed with folate and NADP+ -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qlg | ||||||
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Title | Crystal structure of I14V 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: 1.5 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 | 4qlg.cif.gz | 92.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qlg.ent.gz | 69.1 KB | Display | PDB format |
PDBx/mmJSON format | 4qlg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qlg_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4qlg_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4qlg_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 4qlg_validation.cif.gz | 31.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ql/4qlg ftp://data.pdbj.org/pub/pdb/validation_reports/ql/4qlg | HTTPS FTP |
-Related structure data
Related structure data | 4qleC 4qlfC 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 18005.312 Da / Num. of mol.: 2 / Mutation: I14V 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: 2.16 Å3/Da / Density % sol: 43.18 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris, pH 8.5, 0.1 M LiCl, 34.2% w/v PEG 6000, 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: 1 Å |
Detector | Type: NOIR-1 / Detector: CCD / Date: Dec 18, 2010 |
Radiation | Monochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→73.78 Å / Num. obs: 47127 / % possible obs: 95.6 % / Observed criterion σ(I): 1 / Redundancy: 3.86 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.75 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 3.6 / % possible all: 89.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1RX2 Resolution: 1.5→30.21 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.521 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.094 / 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: 22.307 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→30.21 Å
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Refine LS restraints |
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