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Yorodumi- PDB-4bge: Crystal structure of InhA(S94A) mutant in complex with pyridomycin -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bge | ||||||
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Title | Crystal structure of InhA(S94A) mutant in complex with pyridomycin | ||||||
Components | Enoyl-[acyl-carrier-protein] reductase [NADH] | ||||||
Keywords | OXIDOREDUCTASE | ||||||
Function / homology | Function and homology information 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 / response to antibiotic / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Pojer, F. / Hartkoorn, R.C. / Cole, S.T. | ||||||
Citation | Journal: Nat. Chem. Biol. / Year: 2014 Title: Pyridomycin bridges the NADH- and substrate-binding pockets of the enoyl reductase InhA. Authors: Hartkoorn, R.C. / Pojer, F. / Read, J.A. / Gingell, H. / Neres, J. / Horlacher, O.P. / Altmann, K.H. / Cole, S.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bge.cif.gz | 314.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bge.ent.gz | 257.2 KB | Display | PDB format |
PDBx/mmJSON format | 4bge.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/4bge ftp://data.pdbj.org/pub/pdb/validation_reports/bg/4bge | HTTPS FTP |
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-Related structure data
Related structure data | 4bgiC 4biiC 4dtiS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 28538.781 Da / Num. of mol.: 6 / Mutation: S94A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Gene: inhA, Rv1484, MTCY277.05 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P9WGR1, enoyl-[acyl-carrier-protein] reductase (NADH) #2: Chemical | ChemComp-PYW / #3: 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: 2.32 Å3/Da / Density % sol: 46.93 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 |
Detector | Date: Dec 16, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→50 Å / Num. obs: 140935 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 31.05 Å2 / Rrim(I) all: 0.141 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.25→2.38 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.6 / Rrim(I) all: 0.592 / % possible all: 91.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4DTI Resolution: 2.25→47.5 Å / Cor.coef. Fo:Fc: 0.8173 / Cor.coef. Fo:Fc free: 0.7606 / SU R Cruickshank DPI: 0.395 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.399 / SU Rfree Blow DPI: 0.256 / SU Rfree Cruickshank DPI: 0.258
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Displacement parameters | Biso mean: 33.58 Å2
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Refine analyze | Luzzati coordinate error obs: 0.487 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→47.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.31 Å / Total num. of bins used: 20
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