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Yorodumi- PDB-2pr2: Structure of Mycobacterium tuberculosis enoyl-ACP reductase with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pr2 | ||||||
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Title | Structure of Mycobacterium tuberculosis enoyl-ACP reductase with bound INH-NADP. | ||||||
Components | enoyl-ACP Reductase | ||||||
Keywords | OXIDOREDUCTASE / drug target of isoniazid | ||||||
Function / homology | Function and homology information enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / fatty acid biosynthetic process ...enoyl-[acyl-carrier-protein] reductase activity (NAD(P)H) / trans-2-enoyl-CoA reductase (NADH) activity / mycolic acid biosynthetic process / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / NAD+ binding / peptidoglycan-based cell wall / fatty acid binding / fatty acid biosynthetic process / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Vetting, M.W. / Argyrou, A. / Blanchard, J.S. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2007 Title: New insight into the mechanism of action of and resistance to isoniazid: interaction of Mycobacterium tuberculosis enoyl-ACP reductase with INH-NADP Authors: Argyrou, A. / Vetting, M.W. / Blanchard, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pr2.cif.gz | 66 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pr2.ent.gz | 47.8 KB | Display | PDB format |
PDBx/mmJSON format | 2pr2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pr2_validation.pdf.gz | 758.9 KB | Display | wwPDB validaton report |
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Full document | 2pr2_full_validation.pdf.gz | 766.1 KB | Display | |
Data in XML | 2pr2_validation.xml.gz | 13.3 KB | Display | |
Data in CIF | 2pr2_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pr/2pr2 ftp://data.pdbj.org/pub/pdb/validation_reports/pr/2pr2 | HTTPS FTP |
-Related structure data
Related structure data | 1enyS 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 on special symmetry positions |
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Details | The biological assembly is monomeric and is contained within the assymetric unit. |
-Components
#1: Protein | Mass: 28554.781 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: inhA / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) References: UniProt: P0A5Y6, UniProt: P9WGR1*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH) |
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#2: Chemical | ChemComp-DG1 / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.42 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 9 Details: Cocrystallization with Inh-NADP at 4.8 mM 20 25% of 2-methyl-2,4-pentanediol, 100 mM Bicine pH 9.0., Vapour diffusion under oil, temperature 291K, VAPOR DIFFUSION |
-Data collection
Diffraction | Mean temperature: 193 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 12, 2005 |
Radiation | Monochromator: Rigaku Osmic Blue optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→41 Å / Num. all: 14562 / Num. obs: 14562 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.6 % / Biso Wilson estimate: 51.9 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.055 / Net I/σ(I): 36.7 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 7.5 / Num. unique all: 2077 / Rsym value: 0.353 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ENY Resolution: 2.5→41 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / SU B: 12.636 / SU ML: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.289 / ESU R Free: 0.215 / 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 mean: 37.888 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→41 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 3.648 Å / Origin y: -37.408 Å / Origin z: 18.167 Å
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