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Yorodumi- PDB-3dtg: Structural analysis of mycobacterial branched chain aminotransfer... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dtg | ||||||
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Title | Structural analysis of mycobacterial branched chain aminotransferase- implications for inhibitor design | ||||||
Components | Branched-chain amino acid aminotransferase | ||||||
Keywords | TRANSFERASE / open twisted alpha/beta / Aminotransferase | ||||||
Function / homology | Function and homology information 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 transaminase activity / L-leucine biosynthetic process / valine biosynthetic process ...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 transaminase activity / L-leucine biosynthetic process / valine biosynthetic process / isoleucine biosynthetic process / pyridoxal phosphate binding Similarity search - Function | ||||||
Biological species | Mycobacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Castell, A. / Unge, T. | ||||||
Citation | Journal: To be Published Title: Structural analysis of mycobacterial branched chain aminotransferase - implications for inhibitor design Authors: Castell, A. / Unge, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dtg.cif.gz | 154.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dtg.ent.gz | 120.5 KB | Display | PDB format |
PDBx/mmJSON format | 3dtg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/3dtg ftp://data.pdbj.org/pub/pdb/validation_reports/dt/3dtg | HTTPS FTP |
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-Related structure data
Related structure data | 3dtfS 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: 40366.215 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Gene: ilvE, MSMEG_4276 / Plasmid: pEXP5-CT/TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI References: UniProt: A0R066, branched-chain-amino-acid transaminase #2: Chemical | #3: Chemical | ChemComp-OBZ / | #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: 2.29 Å3/Da / Density % sol: 46.25 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100mM MES-HCl pH 5.5, 300mM Lithium sulfate, 30% (w/v) PEG 4000 , VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 6, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. obs: 57032 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.11 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.4 / Num. unique all: 30903 / Rsym value: 0.41 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3DTF Resolution: 1.9→17 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 19.6 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→17 Å
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Refine LS restraints |
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