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Yorodumi- PDB-4qjz: Pneumocystis carinii dihydrofolate reductase ternary complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qjz | ||||||
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Title | Pneumocystis carinii dihydrofolate reductase ternary complex with NADPH and the inhibitor 24, (N~6~-METHYL-N~6~-(NAPHTHALEN-1-YL)PYRIDO[2,3-D]PYRIMIDINE-2,4,6-TRIAMINE) | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | oxidoreductase/oxidoreductase inhibitor / Rossman fold / hydrolase / NADPH and folate inhibitor / oxidoreductase-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: 1.61 Å | ||||||
Authors | Cody, V. | ||||||
Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015 Title: Structure-activity correlations for three pyrido[2,3-d]pyrimidine antifolates binding to human and Pneumocystis carinii dihydrofolate reductase. Authors: Cody, V. / Pace, J. / Namjoshi, O.A. / Gangjee, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4qjz.cif.gz | 60.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qjz.ent.gz | 42.6 KB | Display | PDB format |
PDBx/mmJSON format | 4qjz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qjz_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4qjz_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4qjz_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 4qjz_validation.cif.gz | 15.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qj/4qjz ftp://data.pdbj.org/pub/pdb/validation_reports/qj/4qjz | HTTPS FTP |
-Related structure data
Related structure data | 4qhvC 4qjcC 4ixeS 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: 23918.537 Da / Num. of mol.: 1 / Fragment: Pneumocystis carinii dihydrofolate reductase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pneumocystis carinii (fungus) / Plasmid: pET_SUMO_pcDHFR / 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-33M / |
#3: Chemical | ChemComp-NDP / |
#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 Å3/Da / Density % sol: 38.58 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6 Details: ProComplex #11: 0.1 M HEPES, pH 7.5, 25% PEG2KMME, VAPOR DIFFUSION, HANGING DROP, temperature 287K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.975 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2013 / 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: 1.53→36.57 Å / Num. all: 66138 / Num. obs: 25824 / % possible obs: 90.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.056 / Net I/σ(I): 8 |
Reflection shell | Resolution: 1.53→1.61 Å / Redundancy: 2.1 % / Rmerge(I) obs: 1.65 / Mean I/σ(I) obs: 0.7 / Num. unique all: 3175 / Rsym value: 0.96 / % possible all: 76.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ixe Resolution: 1.61→35.02 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.344 / SU ML: 0.082 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.118 / ESU R Free: 0.116 / 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: 22.018 Å2
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Refine analyze | Luzzati coordinate error free: 0.205 Å | |||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.61→35.02 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.61→1.652 Å / Total num. of bins used: 20
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