[English] 日本語
Yorodumi- PDB-3hpz: Crystal structure of Mycobacterium tuberculosis LeuA complexed wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hpz | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Mycobacterium tuberculosis LeuA complexed with bromopyruvate | ||||||
Components | 2-isopropylmalate synthase | ||||||
Keywords | TRANSFERASE / 2-isopropylmalate synthase / LeuA / Mycobacterium tuberculosis / inhibitor / inhibition / bromopyruvate / 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: 2.2 Å | ||||||
Authors | Koon, N. / Squire, C.J. / Baker, E.N. | ||||||
Citation | Journal: To be Published Title: Probing the active site of M. tuberculosis LeuA Authors: Koon, N. / Squire, C.J. / Baker, E.N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3hpz.cif.gz | 235.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3hpz.ent.gz | 185.1 KB | Display | PDB format |
PDBx/mmJSON format | 3hpz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/3hpz ftp://data.pdbj.org/pub/pdb/validation_reports/hp/3hpz | HTTPS FTP |
---|
-Related structure data
Related structure data | 3hpsSC 3hq1C S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 70187.430 Da / Num. of mol.: 2 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 |
---|
-Non-polymers , 5 types, 455 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-BPV / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.77 % |
---|---|
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 |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5417 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 15, 2007 / Details: Osmic |
Radiation | Monochromator: Osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5417 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 56200 / Num. obs: 56200 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4981 / % possible all: 87.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3HPS Resolution: 2.2→43.64 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.91 / SU B: 9.528 / SU ML: 0.223 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.303 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 29.814 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→43.64 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.26 Å / Total num. of bins used: 20
|