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Yorodumi- PDB-2bl9: X-ray crystal structure of Plasmodium vivax dihydrofolate reducta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bl9 | ||||||
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Title | X-ray crystal structure of Plasmodium vivax dihydrofolate reductase in complex with pyrimethamine and its derivative | ||||||
Components | DIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE | ||||||
Keywords | OXIDOREDUCTASE / DIHYDROFOLATE REDUCTASE / PLAMODIUM VIVAX / PYRIMETHAMINE / MALARIA / DRUG RESISTANCE | ||||||
Function / homology | Function and homology information thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / methylation Similarity search - Function | ||||||
Biological species | PLASMODIUM VIVAX (malaria parasite P. vivax) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Kongsaeree, P. / Khongsuk, P. / Leartsakulpanich, U. / Chitnumsub, P. / Tarnchompoo, B. / Walkinshaw, M.D. / Yuthavong, Y. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2005 Title: Crystal Structure of Dihydrofolate Reductase from Plasmodium Vivax: Pyrimethamine Displacement Linked with Mutation-Induced Resistance. Authors: Kongsaeree, P. / Khongsuk, P. / Leartsakulpanich, U. / Chitnumsub, P. / Tarnchompoo, B. / Walkinshaw, M.D. / Yuthavong, Y. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bl9.cif.gz | 67.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bl9.ent.gz | 48.2 KB | Display | PDB format |
PDBx/mmJSON format | 2bl9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/2bl9 ftp://data.pdbj.org/pub/pdb/validation_reports/bl/2bl9 | HTTPS FTP |
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-Related structure data
Related structure data | 2blaC 2blbC 2blcC 1j3jS 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: 27110.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PLASMODIUM VIVAX (malaria parasite P. vivax) Production host: ESCHERICHIA COLI (E. coli) References: UniProt: Q9U0E8, UniProt: O02604*PLUS, dihydrofolate reductase |
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#2: Chemical | ChemComp-NDP / |
#3: Chemical | ChemComp-CP6 / |
#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: 2.79 Å3/Da / Density % sol: 55.58 % |
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Crystal grow | Details: 30%PEG4000, 100MM TRIS-HCL, PH 7.2, 10%GLYCEROL |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU R-AXIS / Detector: IMAGE PLATE / Date: Dec 2, 2002 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→30.47 Å / Num. obs: 24170 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 3.21 % / Biso Wilson estimate: 32.3 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 3.19 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.3 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1J3J Resolution: 1.9→30.47 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1288468.64 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.3095 Å2 / ksol: 0.339516 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→30.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
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Xplor file |
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