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Yorodumi- PDB-1bvr: M.TB. ENOYL-ACP REDUCTASE (INHA) IN COMPLEX WITH NAD+ AND C16-FAT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bvr | ||||||
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Title | M.TB. ENOYL-ACP REDUCTASE (INHA) IN COMPLEX WITH NAD+ AND C16-FATTY-ACYL-SUBSTRATE | ||||||
Components | PROTEIN (ENOYL-ACYL CARRIER PROTEIN (ACP) REDUCTASE) | ||||||
Keywords | OXIDOREDUCTASE / NADH-DEPENDENT ENOYL-ACP REDUCTASE / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC | ||||||
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: 2.8 Å | ||||||
Authors | Rozwarski, D.A. / Vilcheze, C. / Sugantino, M. / Bittman, R. / Jacobs, W. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1999 Title: Crystal structure of the Mycobacterium tuberculosis enoyl-ACP reductase, InhA, in complex with NAD+ and a C16 fatty acyl substrate. Authors: Rozwarski, D.A. / Vilcheze, C. / Sugantino, M. / Bittman, R. / Sacchettini, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bvr.cif.gz | 325.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bvr.ent.gz | 266.3 KB | Display | PDB format |
PDBx/mmJSON format | 1bvr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/1bvr ftp://data.pdbj.org/pub/pdb/validation_reports/bv/1bvr | HTTPS FTP |
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-Related structure data
Related structure data | 1enyS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28423.586 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli (E. coli) References: UniProt: P0A5Y6, UniProt: P9WGR1*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH) #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-THT / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 53 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.8 Details: 10% PEG-4000, 6% DMSO, 100 MM AMMONIUM ACETATE, AND 100 MM ADA, PH 6.8 | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: MACSCIENCE / Detector: IMAGE PLATE / Date: Nov 15, 1997 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→10 Å / Num. obs: 30077 / % possible obs: 93 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rsym value: 0.162 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 0.5 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.255 / % possible all: 58 |
Reflection | *PLUS Num. obs: 35800 / Rmerge(I) obs: 0.162 |
Reflection shell | *PLUS % possible obs: 79.3 % / Redundancy: 1 % / Num. unique obs: 3029 / Rmerge(I) obs: 0.255 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ENY Resolution: 2.8→10 Å / Cross valid method: THROUGHOUT / σ(F): 3
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Refinement step | Cycle: LAST / Resolution: 2.8→10 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.9 Å / Total num. of bins used: 10
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 10 Å / σ(F): 3 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / Rfactor Rfree: 0.396 / % reflection Rfree: 10 % / Rfactor Rwork: 0.298 / Rfactor obs: 0.298 |