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Yorodumi- PDB-3jwf: Crystal structure of Bacillus anthracis (Y102F) dihydrofolate red... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jwf | ||||||
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Title | Crystal structure of Bacillus anthracis (Y102F) dihydrofolate reductase complexed with NADPH and (R)-2,4-diamino-5-(3-hydroxy-3-(3,4,5-trimethoxyphenyl)prop-1-ynyl)-6-methylpyrimidine (UCP113A) | ||||||
Components | Dihydrofolate reductase | ||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | ||||||
Function / homology | Function and homology information glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å | ||||||
Authors | Anderson, A.C. / Beierlein, J.M. / Karri, N.G. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2010 Title: Targeted Mutations in Bacillus anthracis Dihydrofolate Reductase Condense Complex Structure-Activity Relationships Authors: Beierlein, J.M. / Karri, N.G. / Anderson, A.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jwf.cif.gz | 87.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jwf.ent.gz | 65.9 KB | Display | PDB format |
PDBx/mmJSON format | 3jwf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jw/3jwf ftp://data.pdbj.org/pub/pdb/validation_reports/jw/3jwf | HTTPS FTP |
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-Related structure data
Related structure data | 3jwcC 3jwkC 3eobS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 3
NCS ensembles :
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-Components
#1: Protein | Mass: 20005.771 Da / Num. of mol.: 2 / Mutation: I2R, Y102F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: BAS2083, BA_2237, dfrA, GBAA2237, GBAA_2237 / Plasmid: pQE2 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q81R22, 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: 2.54 Å3/Da / Density % sol: 51.61 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.75 Details: Initially grown in 25% PEG 10000, 0.1 M MES. Macroseeding in 10% PEG 10000, 0.1 M MES , pH 6.75, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 77.2 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 30, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 |
Reflection | Resolution: 2.57→38.95 Å / Num. all: 12126 / Num. obs: 12126 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 22.8 |
Reflection shell | Resolution: 2.57→2.64 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 4.6 / Num. unique all: 829 / Rsym value: 0.232 / % possible all: 92.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3EOB Resolution: 2.57→38.95 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.892 / SU B: 11.951 / SU ML: 0.251 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 5.146 / ESU R Free: 0.337 / 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: 30.28 Å2
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Refinement step | Cycle: LAST / Resolution: 2.57→38.95 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.57→2.64 Å / Total num. of bins used: 20
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