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Yorodumi- PDB-3i3r: X-ray structure dihydrofolate reductase/thymidylate synthase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3i3r | ||||||
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Title | X-ray structure dihydrofolate reductase/thymidylate synthase from babesia bovis at 2.35A resolution | ||||||
Components | Dihydrofolate reductase/thymidylate synthase | ||||||
Keywords | TRANSFERASE / SSGCID / babesia bovis / dihydrofolate reductase / thymidylate synthase / Methyltransferase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease | ||||||
Function / homology | Function and homology information thymidylate synthase activity / dTMP biosynthetic process / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / methylation / nucleotide binding Similarity search - Function | ||||||
Biological species | Babesia bovis (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2011 Title: Inhibitor-bound complexes of dihydrofolate reductase-thymidylate synthase from Babesia bovis. Authors: Begley, D.W. / Edwards, T.E. / Raymond, A.C. / Smith, E.R. / Hartley, R.C. / Abendroth, J. / Sankaran, B. / Lorimer, D.D. / Myler, P.J. / Staker, B.L. / Stewart, L.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3i3r.cif.gz | 200.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3i3r.ent.gz | 159.7 KB | Display | PDB format |
PDBx/mmJSON format | 3i3r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/3i3r ftp://data.pdbj.org/pub/pdb/validation_reports/i3/3i3r | HTTPS FTP |
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-Related structure data
Related structure data | 3k2hC 3nrrC 1qzfS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 58283.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Babesia bovis (eukaryote) / Strain: T2Bo / Gene: BBOV_II000780 / Plasmid: PET28-HISSMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A7ASX7, thymidylate synthase #2: Chemical | #3: 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: 2.6 Å3/Da / Density % sol: 53 % |
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Crystal grow | Temperature: 290 K / Method: microfludic microbatch in a crystal card / pH: 9.5 Details: WIZARD SCREEN A1: 20% PEG 8000, 100MM CHES PH 9.5; BABOA.01191.A AT 11.3MG/ML, MICROFLUDIC MICROBATCH IN A CRYSTAL CARD, TEMPERATURE 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 17, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→72.2 Å / Num. all: 47995 / Num. obs: 47995 / % possible obs: 96.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 9.64 |
Reflection shell | Resolution: 2.35→2.41 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 2.2 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1QZF modified by the ccp4 program chainsaw Resolution: 2.35→19.69 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.9 / SU B: 7.15 / SU ML: 0.172 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.365 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.29 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→19.69 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.35→2.41 Å / Total num. of bins used: 20
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