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Yorodumi- PDB-3gn1: Structure of Pteridine Reductase 1 (PTR1) from TRYPANOSOMA BRUCEI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3gn1 | ||||||
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Title | Structure of Pteridine Reductase 1 (PTR1) from TRYPANOSOMA BRUCEI in ternary complex with cofactor (NADP+) and inhibitor (DDD00067116) | ||||||
Components | Pteridine reductase | ||||||
Keywords | OXIDOREDUCTASE / PTERIDINE REDUCTASE / PTR1 / TRYPANOSOMA BRUCEI / SHORT CHAIN DEHYDROGENASE / INHIBITOR | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Trypanosoma brucei brucei (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Tulloch, L.B. / Brenk, R. / Hunter, W.N. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2009 Title: One scaffold, three binding modes: novel and selective pteridine reductase 1 inhibitors derived from fragment hits discovered by virtual screening. Authors: Mpamhanga, C.P. / Spinks, D. / Tulloch, L.B. / Shanks, E.J. / Robinson, D.A. / Collie, I.T. / Fairlamb, A.H. / Wyatt, P.G. / Frearson, J.A. / Hunter, W.N. / Gilbert, I.H. / Brenk, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3gn1.cif.gz | 218.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3gn1.ent.gz | 182.9 KB | Display | PDB format |
PDBx/mmJSON format | 3gn1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/3gn1 ftp://data.pdbj.org/pub/pdb/validation_reports/gn/3gn1 | 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: 30685.787 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Gene: PTR1 / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O76290 #2: Chemical | ChemComp-NAP / #3: Chemical | #4: Chemical | #5: 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: 2.05 Å3/Da / Density % sol: 39.89 % |
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Crystal grow | Method: vapor diffusion / pH: 4.5 Details: 2-3M SODIUM ACETATE, 10-100MM SODIUM CITRATE, PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→30.66 Å / Num. obs: 63246 / % possible obs: 94.8 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.051 / Rsym value: 0.051 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.136 / Mean I/σ(I) obs: 5.1 / Rsym value: 0.136 / % possible all: 89.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30.66 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.616 / SU ML: 0.124 / TLS residual ADP flag: LIKELY RESIDUAL / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: ALL OF THE 17 RELATED STRUCTURES ARE EXPRESSED FROM THE SAME DNA CONSTRUCT, WHICH ENCODES CYS AT POSITIONS 59 AND 168. CRYSTALS HARVESTED WITHIN A COUPLE OF DAYS OF FORMATION CONTAIN CYS AT ...Details: ALL OF THE 17 RELATED STRUCTURES ARE EXPRESSED FROM THE SAME DNA CONSTRUCT, WHICH ENCODES CYS AT POSITIONS 59 AND 168. CRYSTALS HARVESTED WITHIN A COUPLE OF DAYS OF FORMATION CONTAIN CYS AT POSITIONS 59 AND 168. HOWEVER THESE TWO RESIDUES APPEAR QUITE REACTIVE AND OVER TIME BECOME OXIDISED TO CSX, AS DETERMINED BY THE EMERGENCE IN OLDER CRYSTALS OF ELECTRON DENSITY FOR THE OD ATOM. SOMETIMES CYS168 REACTS WITH DTT IN THE CRYSTALLISATION BUFFER, COVALENTLY LINKING THE TWO MOLECULES BY AN S-S BOND.
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Solvent computation | Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.03 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.05 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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