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Yorodumi- PDB-3fig: Crystal Structure of Leucine-bound LeuA from Mycobacterium tuberc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fig | ||||||
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Title | Crystal Structure of Leucine-bound LeuA from Mycobacterium tuberculosis | ||||||
Components | 2-isopropylmalate synthase | ||||||
Keywords | TRANSFERASE / TIM barrel / Amino-acid biosynthesis / Branched-chain amino acid biosynthesis / Leucine biosynthesis | ||||||
Function / homology | Function and homology information 2-isopropylmalate synthase / 2-isopropylmalate synthase activity / acetyl-CoA C-acetyltransferase activity / L-leucine biosynthetic process / potassium ion binding / manganese ion binding / magnesium ion binding / zinc ion binding / extracellular region / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Koon, N. / Squire, C.J. / Baker, E.N. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 Title: Crystal structure of LeuA from Mycobacterium tuberculosis, a key enzyme in leucine biosynthesis. Authors: Koon, N. / Squire, C.J. / Baker, E.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fig.cif.gz | 235.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fig.ent.gz | 186 KB | Display | PDB format |
PDBx/mmJSON format | 3fig.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/3fig ftp://data.pdbj.org/pub/pdb/validation_reports/fi/3fig | HTTPS FTP |
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-Related structure data
Related structure data | 1sr9SC S: Starting model for refinement C: citing same article (ref.) |
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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: 70285.531 Da / Num. of mol.: 2 / Mutation: T2A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: leuA / Plasmid: pProExHta / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus RP References: UniProt: P96420, UniProt: P9WQB3*PLUS, 2-isopropylmalate synthase #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ZN / | #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: 2.03 Å3/Da / Density % sol: 39.27 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Sodium Citrate, MPEG 2000, pH 6.0, Vapor diffusion, sitting drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 49393 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SR9 Resolution: 2.3→27.66 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 7.465 / SU ML: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.368 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 60.56 Å2 / Biso mean: 27.572 Å2 / Biso min: 6.03 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→27.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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