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- PDB-3bmc: Structure of Pteridine Reductase 1 (PTR1) from Trypanosoma brucei... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3bmc | ||||||
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Title | Structure of Pteridine Reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor (NADP+) and substrate (folate) | ||||||
![]() | (Pteridine reductase) x 2 | ||||||
![]() | OXIDOREDUCTASE / pteridine reductase / ptr1 / trypanosoma brucei / short chain dehydrogenase / substrate / folate | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tulloch, L.B. / Hunter, W.N. | ||||||
![]() | ![]() Title: Structure-based design of pteridine reductase inhibitors targeting african sleeping sickness and the leishmaniases. Authors: Tulloch, L.B. / Martini, V.P. / Iulek, J. / Huggan, J.K. / Lee, J.H. / Gibson, C.L. / Smith, T.K. / Suckling, C.J. / Hunter, W.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 201.7 KB | Display | ![]() |
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PDB format | ![]() | 168.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
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Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 43.7 KB | Display | |
Data in CIF | ![]() | 57.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bmnC ![]() 3bmoC ![]() 3bmqC ![]() 3jq6C ![]() 3jq7C ![]() 3jq8C ![]() 3jq9C ![]() 3jqaC ![]() 3jqbC ![]() 3jqcC ![]() 3jqdC ![]() 3jqeC ![]() 3jqfC ![]() 3jqgC ![]() 3bms ![]() 3bmt C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: GLU / End label comp-ID: FOL / Refine code: 1 / Auth seq-ID: 2 - 270 / Label seq-ID: 22 - 1
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Components
#1: Protein | Mass: 30685.787 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Protein | Mass: 30669.791 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-NAP / #4: Chemical | ChemComp-FOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / 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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→73.737 Å / Num. obs: 23556 / % possible obs: 81.1 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 9.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() 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 | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.712 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→37.67 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 1784 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.6→2.668 Å / Total num. of bins used: 20
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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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