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Yorodumi- PDB-2c7v: Structure of Trypanosoma brucei pteridine reductase (PTR1) in ter... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c7v | ||||||
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Title | Structure of Trypanosoma brucei pteridine reductase (PTR1) in ternary complex with cofactor and the antifolate methotrexate | ||||||
Components | PTERIDINE REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / PTERIDINE REDUCTASE / TRYPANOSOMATIDS / DRUG RESISTANCE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE / METHOTREXATE RESISTANCE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | TRYPANOSOMA BRUCEI BRUCEI (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Dawson, A. / Gibellini, F. / Sienkiewicz, N. / Fyfe, P.K. / McLuskey, K. / Fairlamb, A.H. / Hunter, W.N. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2006 Title: Structure and Reactivity of Trypanosoma Brucei Pteridine Reductase: Inhibition by the Archetypal Antifolate Methotrexate Authors: Dawson, A. / Gibellini, F. / Sienkiewicz, N. / Tulloch, L.B. / Fyfe, P.K. / Mcluskey, K. / Fairlamb, A.H. / 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 | 2c7v.cif.gz | 228.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c7v.ent.gz | 184.2 KB | Display | PDB format |
PDBx/mmJSON format | 2c7v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c7v_validation.pdf.gz | 2.6 MB | Display | wwPDB validaton report |
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Full document | 2c7v_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 2c7v_validation.xml.gz | 35.9 KB | Display | |
Data in CIF | 2c7v_validation.cif.gz | 51.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/2c7v ftp://data.pdbj.org/pub/pdb/validation_reports/c7/2c7v | HTTPS FTP |
-Related structure data
Related structure data | 1e92S S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 28738.406 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Plasmid: PET-TBPTR1H / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O76290, pteridine reductase |
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-Non-polymers , 5 types, 811 molecules
#2: Chemical | ChemComp-NAP / #3: Chemical | ChemComp-MTX / #4: Chemical | #5: Chemical | #6: 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: 2.01 Å3/Da / Density % sol: 38.22 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7 Details: PROTEIN BUFFER WAS 20 MM TRIS HCL, PH 7.0 WITH 1MM NADP, 1 MM METHOTREXATE AND 20 MM DITHIOTHREITOL, PROTEIN CONCENTRATION WAS 6 MG/ML. HANGING DROP RESERVOIR SOLUTION WAS 0.1 M SODIUM ...Details: PROTEIN BUFFER WAS 20 MM TRIS HCL, PH 7.0 WITH 1MM NADP, 1 MM METHOTREXATE AND 20 MM DITHIOTHREITOL, PROTEIN CONCENTRATION WAS 6 MG/ML. HANGING DROP RESERVOIR SOLUTION WAS 0.1 M SODIUM CACODYLATE PH 6.5 AND 1.4 M SODIUM ACETATE. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jul 30, 2004 / 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: 2.2→74.5 Å / Num. obs: 50048 / % possible obs: 99.2 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 3.5 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PBD ENTRY 1E92 Resolution: 2.2→74.54 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.551 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.303 / ESU R Free: 0.218 / 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: 24.22 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→74.54 Å
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Refine LS restraints |
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