+Open data
-Basic information
Entry | Database: PDB / ID: 8gil | |||||||||
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Title | L-threonine 3-Dehydrogenase from Trypanosoma cruzi (apo form) | |||||||||
Components | L-threonine 3-dehydrogenase | |||||||||
Keywords | OXIDOREDUCTASE / threonine / dehydrogenase / trypanossoma / apo | |||||||||
Function / homology | NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding domain superfamily / : / L-threonine 3-dehydrogenase, putative Function and homology information | |||||||||
Biological species | Trypanosoma cruzi (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Faria, J.N. / Mercaldi, G.F. / Fagundes, M. / Bezerra, E.H.S. / Cordeiro, A.T. | |||||||||
Funding support | Brazil, 2items
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Citation | Journal: To Be Published Title: Structure, allosteric regulation and metabolic activity of L-threonine 3-Dehydrogenase from Trypanosoma cruzi Authors: Faria, J.N. / Mercaldi, G.F. / Fagundes, M. / Eufrasio, A.G. / Cordeiro, A.T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8gil.cif.gz | 243 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8gil.ent.gz | 193.9 KB | Display | PDB format |
PDBx/mmJSON format | 8gil.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8gil_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8gil_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8gil_validation.xml.gz | 24 KB | Display | |
Data in CIF | 8gil_validation.cif.gz | 33.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gi/8gil ftp://data.pdbj.org/pub/pdb/validation_reports/gi/8gil | HTTPS FTP |
-Related structure data
Related structure data | 8gjbC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 40503.523 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: Tc00.1047053507923.10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4CU39, L-threonine 3-dehydrogenase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 1.976 Å3/Da / Density % sol: 37.781 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 25% PEG 3350, 200 mM ammonium acetate and 100 mM Bis-Tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97718 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 2, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97718 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→46.73 Å / Num. obs: 36424 / % possible obs: 99.1 % / Redundancy: 4.7 % / CC1/2: 0.995 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.1→2.16 Å / Redundancy: 4.5 % / Num. unique obs: 2927 / CC1/2: 0.595 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.727 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.917 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.213 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.969 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→46.727 Å
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Refine LS restraints |
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LS refinement shell |
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