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Yorodumi- PDB-3hpx: Crystal structure of Mycobacterium tuberculosis LeuA active site ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hpx | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis LeuA active site domain 1-425 (truncation mutant delta:426-644) | ||||||
Components | 2-isopropylmalate synthase | ||||||
Keywords | TRANSFERASE / 2-isopropylmalate synthase / LeuA / Mycobacterium tuberculosis / truncation mutant / active site domain / 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: 2.03 Å | ||||||
Authors | Koon, N. / Squire, C.J. / Baker, E.N. | ||||||
Citation | Journal: Biochemistry / Year: 2012 Title: Removal of the C-terminal regulatory domain of alpha-isopropylmalate synthase disrupts functional substrate binding Authors: Huisman, F.H. / Koon, N. / Bulloch, E.M. / Baker, H.M. / Baker, E.N. / Squire, C.J. / Parker, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hpx.cif.gz | 180.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hpx.ent.gz | 140.8 KB | Display | PDB format |
PDBx/mmJSON format | 3hpx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/3hpx ftp://data.pdbj.org/pub/pdb/validation_reports/hp/3hpx | HTTPS FTP |
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-Related structure data
Related structure data | 3rmjC 3u6wC 1sr9S 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: 47537.293 Da / Num. of mol.: 2 / Fragment: Active site domain: UNP residues 1-425 / Mutation: Truncation mutant delta:426-644 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: leuA, MT3813, MTV025.058, Rv3710 / Plasmid: pPROEXHTa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P96420, UniProt: P9WQB3*PLUS, 2-isopropylmalate synthase #2: Chemical | #3: Chemical | #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: 2.09 Å3/Da / Density % sol: 41.23 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.25 Details: Sodium citrate, PEG MME 2000, pH 6.25, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 10, 2005 / Details: Osmic |
Radiation | Monochromator: Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→30 Å / Num. all: 47066 / Num. obs: 47066 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 2.03→2.1 Å / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 3.8 / Num. unique all: 4222 / % possible all: 84.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1SR9 Resolution: 2.03→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.562 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.237 / ESU R Free: 0.198 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.097 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.03→2.08 Å / Total num. of bins used: 20
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