+Open data
-Basic information
Entry | Database: PDB / ID: 3u6w | ||||||
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Title | Truncated M. tuberculosis LeuA (1-425) complexed with KIV | ||||||
Components | 2-isopropylmalate synthase | ||||||
Keywords | TRANSFERASE / TIM barrel | ||||||
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: 2.21 Å | ||||||
Authors | Koon, N. / Baker, E.N. / Squire, C.J. | ||||||
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 | 3u6w.cif.gz | 166.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3u6w.ent.gz | 129.6 KB | Display | PDB format |
PDBx/mmJSON format | 3u6w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3u6w_validation.pdf.gz | 464.8 KB | Display | wwPDB validaton report |
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Full document | 3u6w_full_validation.pdf.gz | 470.8 KB | Display | |
Data in XML | 3u6w_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 3u6w_validation.cif.gz | 43.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u6/3u6w ftp://data.pdbj.org/pub/pdb/validation_reports/u6/3u6w | HTTPS FTP |
-Related structure data
Related structure data | 3hpxSC 3rmjC 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: 47665.422 Da / Num. of mol.: 2 / Fragment: catalytic domain (UNP residues 1-425) 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)pRP References: UniProt: P96420, UniProt: P9WQB3*PLUS, 2-isopropylmalate synthase #2: Chemical | #3: Chemical | #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: 2.06 Å3/Da / Density % sol: 40.15 % |
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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 12, 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: 2.2→30 Å / Num. all: 35261 / Num. obs: 35261 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.278 / Mean I/σ(I) obs: 3.7 / % possible all: 72.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3HPX Resolution: 2.21→29.26 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.835 / SU B: 7.633 / SU ML: 0.198 / Cross valid method: THROUGHOUT / ESU R Free: 0.3 / 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: 11.472 Å2
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Refinement step | Cycle: LAST / Resolution: 2.21→29.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.213→2.27 Å / Total num. of bins used: 20
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