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Yorodumi- PDB-5u3f: Structure of Mycobacterium tuberculosis IlvE, a branched-chain am... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5u3f | |||||||||
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Title | Structure of Mycobacterium tuberculosis IlvE, a branched-chain amino acid transaminase, in complex with D-cycloserine derivative | |||||||||
Components | Branched-chain-amino-acid aminotransferase | |||||||||
Keywords | TRANSFERASE / branched-chain amino acid transaminase / amino acid biosynthesis / Pyridoxal phosphate / inhibitor / D-cycloserine | |||||||||
Function / homology | Function and homology information L-methionine salvage / branched-chain amino acid metabolic process / protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine / L-leucine:2-oxoglutarate aminotransferase activity / branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / branched-chain amino acid biosynthetic process / branched-chain-amino-acid transaminase activity ...L-methionine salvage / branched-chain amino acid metabolic process / protein-pyridoxal-5-phosphate linkage via peptidyl-N6-pyridoxal phosphate-L-lysine / L-leucine:2-oxoglutarate aminotransferase activity / branched-chain-amino-acid transaminase / L-leucine transaminase activity / L-valine transaminase activity / L-isoleucine transaminase activity / branched-chain amino acid biosynthetic process / branched-chain-amino-acid transaminase activity / L-leucine biosynthetic process / valine biosynthetic process / isoleucine biosynthetic process / pyridoxal phosphate binding Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.695 Å | |||||||||
Authors | Favrot, L. / Amorim Franco, T.M. / Blanchard, J.S. | |||||||||
Funding support | United States, Brazil, 2items
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Citation | Journal: ACS Chem. Biol. / Year: 2017 Title: Mechanism-Based Inhibition of the Mycobacterium tuberculosis Branched-Chain Aminotransferase by d- and l-Cycloserine. Authors: Amorim Franco, T.M. / Favrot, L. / Vergnolle, O. / Blanchard, J.S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5u3f.cif.gz | 153.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5u3f.ent.gz | 117.3 KB | Display | PDB format |
PDBx/mmJSON format | 5u3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5u3f_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5u3f_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5u3f_validation.xml.gz | 30.6 KB | Display | |
Data in CIF | 5u3f_validation.cif.gz | 46.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u3/5u3f ftp://data.pdbj.org/pub/pdb/validation_reports/u3/5u3f | HTTPS FTP |
-Related structure data
Related structure data | 3ht5S 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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-Components
#1: Protein | Mass: 39706.910 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: ilvE, Rv2210c, MTCY190.21c / Production host: Escherichia coli (E. coli) References: UniProt: P9WQ75, branched-chain-amino-acid transaminase #2: Chemical | #3: 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: 1.89 Å3/Da / Density % sol: 34.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bis-Tris, pH 6.5 and 25 % w/v polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å |
Detector | Type: RAYONIX MX325HE / Detector: CCD / Date: Jun 11, 2015 |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 1.695→50 Å / Num. obs: 117641 / % possible obs: 91.1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 12.51 |
Reflection shell | Resolution: 1.695→1.8 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 2.4 / % possible all: 98.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HT5 Resolution: 1.695→36.265 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.06 / Phase error: 21.59
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.695→36.265 Å
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Refine LS restraints |
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LS refinement shell |
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