+Open data
-Basic information
Entry | Database: PDB / ID: 4ixf | ||||||
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Title | pcDHFR-269 F69N variant | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE/Inhibitor / pcDHFR-269-NADPH F69N ternary complex / reductase / OXIDOREDUCTASE-Inhibitor complex | ||||||
Function / homology | Function and homology information dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | Pneumocystis carinii (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Cody, V. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Design, Synthesis, and Molecular Modeling of Novel Pyrido[2,3-d]pyrimidine Analogues As Antifolates; Application of Buchwald-Hartwig Aminations of Heterocycles. Authors: Gangjee, A. / Namjoshi, O.A. / Raghavan, S. / Queener, S.F. / Kisliuk, R.L. / Cody, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ixf.cif.gz | 61.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ixf.ent.gz | 43.2 KB | Display | PDB format |
PDBx/mmJSON format | 4ixf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ixf_validation.pdf.gz | 994.8 KB | Display | wwPDB validaton report |
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Full document | 4ixf_full_validation.pdf.gz | 997.4 KB | Display | |
Data in XML | 4ixf_validation.xml.gz | 12 KB | Display | |
Data in CIF | 4ixf_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/4ixf ftp://data.pdbj.org/pub/pdb/validation_reports/ix/4ixf | HTTPS FTP |
-Related structure data
Related structure data | 4ixeC 4ixgC 3cd2S S: Starting model for refinement C: citing same article (ref.) |
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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: 23885.465 Da / Num. of mol.: 1 / Mutation: F69N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pneumocystis carinii (fungus) / Plasmid: pET-SUMO-pcDHFR-F69N / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta Gami B (DE3) / References: UniProt: P16184, dihydrofolate reductase |
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#2: Chemical | ChemComp-NDP / |
#3: Chemical | ChemComp-IXF / |
#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: 2.03 Å3/Da / Density % sol: 39.34 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 35% PEG 2000, 49 mM MES, 100 mM KCl, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.975 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 19, 2011 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.975 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→37.2 Å / Num. obs: 21146 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Rsym value: 0.049 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.4 / Rsym value: 0.38 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3CD2 Resolution: 1.7→37.2 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.811 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 28.485 Å2
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Refine analyze | Luzzati d res low obs: 0.208 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→37.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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