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Yorodumi- PDB-7u0m: Crystal structure of a enoyl-[acyl-carrier-protein] reductase (In... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7u0m | ||||||
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Title | Crystal structure of a enoyl-[acyl-carrier-protein] reductase (InhA) from Mycobacterium abscessus bound to NAD and NITD-916 | ||||||
Components | Enoyl-[acyl-carrier-protein] reductase [NADH] | ||||||
Keywords | OXIDOREDUCTASE / InhA / Mycobacterium / tuberculosis / cystic fibrosis / CF / pulmonary infections / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID | ||||||
Function / homology | Function and homology information trans-2-enoyl-CoA reductase (NADH) activity / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide binding Similarity search - Function | ||||||
Biological species | Mycobacteroides abscessus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Funding support | United States, 1items
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Citation | Journal: Acs Infect Dis. / Year: 2022 Title: Efficacy and Mode of Action of a Direct Inhibitor of Mycobacterium abscessus InhA. Authors: Alcaraz, M. / Roquet-Baneres, F. / Leon-Icaza, S.A. / Abendroth, J. / Boudehen, Y.M. / Cougoule, C. / Edwards, T.E. / Kremer, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7u0m.cif.gz | 238.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u0m.ent.gz | 188.5 KB | Display | PDB format |
PDBx/mmJSON format | 7u0m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u0/7u0m ftp://data.pdbj.org/pub/pdb/validation_reports/u0/7u0m | HTTPS FTP |
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-Related structure data
Related structure data | 7kliC 7l6cSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
-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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-Components
#1: Protein | Mass: 29695.074 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacteroides abscessus (bacteria) / Gene: MAB_2722c / Production host: Escherichia coli (E. coli) References: UniProt: B1MC30, enoyl-[acyl-carrier-protein] reductase (NADH) #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.37 Å3/Da / Density % sol: 48.05 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: MyabA.00170.a.B1.PS38577 at 23.06 mg/mL with 3.5 mM NAD and 3.5 mM NITD-916 against the Index Screen condition H10: 0.2 M sodium citrate tribasic, 20% ethylene glycol supplemented with ...Details: MyabA.00170.a.B1.PS38577 at 23.06 mg/mL with 3.5 mM NAD and 3.5 mM NITD-916 against the Index Screen condition H10: 0.2 M sodium citrate tribasic, 20% ethylene glycol supplemented with compounds as cryo-protectant, crystal ID 323195h10, unique puck ID tdn4-6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Nov 4, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.45→41.32 Å / Num. obs: 95830 / % possible obs: 98.2 % / Redundancy: 3.949 % / Biso Wilson estimate: 11.58 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.053 / Χ2: 0.975 / Net I/σ(I): 18.13 / Num. measured all: 378452 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7l6c Resolution: 1.45→41.32 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.09 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 78.5 Å2 / Biso mean: 17.0017 Å2 / Biso min: 5.44 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.45→41.32 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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