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Yorodumi- PDB-5vrl: CRYSTAL STRUCTURE OF THE INHA FROM MYCOBACTERIUM TUBERCULOSIS IN ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vrl | ||||||
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Title | CRYSTAL STRUCTURE OF THE INHA FROM MYCOBACTERIUM TUBERCULOSIS IN COMPLEX WITH AN12855, EBSI 4333. | ||||||
Components | Enoyl-[acyl-carrier-protein] reductase [NADH] | ||||||
Keywords | OXIDOREDUCTASE / INHA / ENOYL-ACYL REDUCTASE / TUBERCULOSIS | ||||||
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 / response to antibiotic Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | ||||||
Authors | Abendroth, J. / Edwards, T.E. / Lorimer, D. | ||||||
Funding support | United States, 1items
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Citation | Journal: Life Sci Alliance / Year: 2018 Title: Discovery of a cofactor-independent inhibitor ofMycobacterium tuberculosisInhA. Authors: Xia, Y. / Zhou, Y. / Carter, D.S. / McNeil, M.B. / Choi, W. / Halladay, J. / Berry, P.W. / Mao, W. / Hernandez, V. / O'Malley, T. / Korkegian, A. / Sunde, B. / Flint, L. / Woolhiser, L.K. / ...Authors: Xia, Y. / Zhou, Y. / Carter, D.S. / McNeil, M.B. / Choi, W. / Halladay, J. / Berry, P.W. / Mao, W. / Hernandez, V. / O'Malley, T. / Korkegian, A. / Sunde, B. / Flint, L. / Woolhiser, L.K. / Scherman, M.S. / Gruppo, V. / Hastings, C. / Robertson, G.T. / Ioerger, T.R. / Sacchettini, J. / Tonge, P.J. / Lenaerts, A.J. / Parish, T. / Alley, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5vrl.cif.gz | 114.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vrl.ent.gz | 88.3 KB | Display | PDB format |
PDBx/mmJSON format | 5vrl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vrl_validation.pdf.gz | 778.5 KB | Display | wwPDB validaton report |
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Full document | 5vrl_full_validation.pdf.gz | 779 KB | Display | |
Data in XML | 5vrl_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 5vrl_validation.cif.gz | 15 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/5vrl ftp://data.pdbj.org/pub/pdb/validation_reports/vr/5vrl | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 28837.057 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh) (bacteria) Strain: CDC 1551 / Oshkosh / Gene: inhA, MT1531 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P9WGR0, enoyl-[acyl-carrier-protein] reductase (NADH) |
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#2: Chemical | ChemComp-9JA / (~{ |
#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: 3.54 Å3/Da / Density % sol: 65.23 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.8 Details: INHA, ENOYL-ACP REDUCTASE FROM MYCOBACTERIUM TUBERCULOSIS, R5645 AT 10.0 MG/ML (350UM), BATCH NUMBER 1605003A, IN 20MM PIPES PH 7.3, 50 MM NACL, WITH 0.88MM AN12855 (EBSI4333) AGAINST ...Details: INHA, ENOYL-ACP REDUCTASE FROM MYCOBACTERIUM TUBERCULOSIS, R5645 AT 10.0 MG/ML (350UM), BATCH NUMBER 1605003A, IN 20MM PIPES PH 7.3, 50 MM NACL, WITH 0.88MM AN12855 (EBSI4333) AGAINST RIGAKUREAGENTS MORPHEUS SCREEN D6: 10% PEG 8000, 20% ETHYLENE GLYCOL, 100MM MOPS/HEPES-NA PH 7.5, 20MM EACH 1,6-HEXANEDIOL, 1-BUTANOL, (RS)-1,2-PROPANEDIOL, 2- PROPANOL, 1,4-BUTANEDIOL, 1,3-PROPANEDIOL; DIRECT CRYO; CRYSTAL TRACKING ID 254099C3 (VXD5-6), PH 6.80, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K PH range: 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 17, 2014 |
Radiation | Monochromator: DIAMOND [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9787 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→41.9 Å / Num. obs: 12988 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 9 % / Biso Wilson estimate: 57.68 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 26.8 |
Reflection shell | Resolution: 2.65→2.72 Å / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 3.8 / % possible all: 100 |
-Processing
Software | Name: PHENIX / Version: 1.9_1675 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→41.9 Å / Cross valid method: THROUGHOUT
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Solvent computation | Shrinkage radii: 0.9 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 58.93 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→41.9 Å
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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