+Open data
-Basic information
Entry | Database: PDB / ID: 2x9v | ||||||
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Title | High resolution structure of TbPTR1 with trimetrexate | ||||||
Components | PTERIDINE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / SHORT CHAIN DEHYDROGENASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | TRYPANOSOMA BRUCEI BRUCEI (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.3 Å | ||||||
Authors | Dawson, A. / Tulloch, L.B. / Barrack, K.L. / Hunter, W.N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2010 Title: High-Resolution Structures of Trypanosoma Brucei Pteridine Reductase Ligand Complexes Inform on the Placement of New Molecular Entities in the Active Site of a Potential Drug Target Authors: Dawson, A. / Tulloch, L.B. / Barrack, K.L. / Hunter, W.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x9v.cif.gz | 436.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x9v.ent.gz | 374.9 KB | Display | PDB format |
PDBx/mmJSON format | 2x9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x9/2x9v ftp://data.pdbj.org/pub/pdb/validation_reports/x9/2x9v | HTTPS FTP |
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-Related 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: 30669.791 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Plasmid: PET15B_TBPTR1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O76290, pteridine reductase #2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-TMQ / #4: Chemical | ChemComp-ACT / #5: Water | ChemComp-HOH / | Sequence details | ADDITIONAL | |
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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: 2.05 Å3/Da / Density % sol: 40.1 % / Description: REFINEMENT STARTED DIRECTLY USING PDB 2C7V |
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Crystal grow | pH: 7.5 Details: PROTEIN BUFFER CONTAINED 20MM TRIS PH7.5. RESERVOIR CONTAINED 2.5M SODIUM ACETATE, 50MM SODIUM CITRATE PH4.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 16, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→31.05 Å / Num. obs: 239044 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 9.96 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 1.3→1.37 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.6 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: NONE Resolution: 1.3→31.05 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.175 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.041 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 10.426 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→31.05 Å
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