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Yorodumi- PDB-1mxf: Crystal Structure of Inhibitor Complex of Putative Pteridine Redu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mxf | ||||||
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Title | Crystal Structure of Inhibitor Complex of Putative Pteridine Reductase 2 (PTR2) from Trypanosoma cruzi | ||||||
Components | PTERIDINE REDUCTASE 2 | ||||||
Keywords | OXIDOREDUCTASE / SDR TOPOLOGY / PROTEIN-INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å | ||||||
Authors | Schormann, N. / Pal, B. / Senkovich, O. / Carson, M. / Howard, A. / Smith, C. / Delucas, L. / Chattopadhyay, D. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2005 Title: Crystal structure of Trypanosoma cruzi pteridine reductase 2 in complex with a substrate and an inhibitor. Authors: Schormann, N. / Pal, B. / Senkovich, O. / Carson, M. / Howard, A. / Smith, C. / Delucas, L. / Chattopadhyay, D. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2001 Title: Expression, purification, crystallization and preliminary crystallographic analysis of recombinant pteridine reductase of Trypanosoma cruzi Authors: Schormann, N. / Pal, B. / Chattopadhyay, D. | ||||||
History |
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Remark 999 | sequence the sequence of this molecule is not yet deposited in any sequence database |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mxf.cif.gz | 198.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mxf.ent.gz | 169.8 KB | Display | PDB format |
PDBx/mmJSON format | 1mxf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mx/1mxf ftp://data.pdbj.org/pub/pdb/validation_reports/mx/1mxf | 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: 29321.957 Da / Num. of mol.: 4 / Fragment: pteridine reductase Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Strain: Sylvio, X10 / Gene: ptr2 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): B834pLysS / References: UniProt: Q8I814 #2: Chemical | ChemComp-NDP / #3: Chemical | ChemComp-MTX / #4: 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: 2.3 Å3/Da / Density % sol: 46.7 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / pH: 6.3 Details: Sodium acetate, cacodylate buffer, pH 6.30, temperature 293K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 8 / Method: vapor diffusion, hanging dropDetails: Schormann, N., (2001) Acta Crystallogr.,Sect.D, 57, 1671. | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9537, 0.9791, 0.9792 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 20, 2000 / Details: MIRRORS | ||||||||||||
Radiation | Monochromator: GRAPHITE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.76→36 Å / Num. obs: 89619 / % possible obs: 80 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.037 / Net I/σ(I): 11.8 | ||||||||||||
Reflection | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 50 Å / Num. obs: 48846 / % possible obs: 97.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.084 | ||||||||||||
Reflection shell | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 2.44 Å / % possible obs: 91.9 % / Redundancy: 1.9 % / Num. unique obs: 7734 / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 3.2 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.3→19.49 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 187450.3 / Data cutoff high rms absF: 187450.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: ENGH & HUBER
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.982 Å2 / ksol: 0.335 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→19.49 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 50 Å / Rfactor Rfree: 0.247 / Rfactor Rwork: 0.204 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.308 / Rfactor Rwork: 0.274 |