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Yorodumi- PDB-5vrm: CRYSTAL STRUCTURE OF THE INHA FROM MYCOBACTERIUM TUBERCULOSIS IN ... -
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-Basic information
Entry | Database: PDB / ID: 5vrm | ||||||
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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: 2.5 Å | ||||||
Authors | Abendroth, J. / Edwards, T.E. / Lorimer, D. | ||||||
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 | 5vrm.cif.gz | 386.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vrm.ent.gz | 320.4 KB | Display | PDB format |
PDBx/mmJSON format | 5vrm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vrm_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5vrm_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5vrm_validation.xml.gz | 37.6 KB | Display | |
Data in CIF | 5vrm_validation.cif.gz | 49.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/5vrm ftp://data.pdbj.org/pub/pdb/validation_reports/vr/5vrm | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 28837.057 Da / Num. of mol.: 4 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) #2: Chemical | ChemComp-9JJ / [[( #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: 2.47 Å3/Da / Density % sol: 50.24 % |
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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 (340UM), BATCH NUMBER 1526003A, IN 20MM PIPES PH 7.3, 50 MM NACL, WITH 3.5MM NAD+ (EBSI1606) AND 420UM AN2918 ...Details: INHA, ENOYL-ACP REDUCTASE FROM MYCOBACTERIUM TUBERCULOSIS, R5645 AT 10.0 MG/ML (340UM), BATCH NUMBER 1526003A, IN 20MM PIPES PH 7.3, 50 MM NACL, WITH 3.5MM NAD+ (EBSI1606) AND 420UM AN2918 (EBSI4012) AGAINST OPTIMIZATION SCREEN ACR_PEGISH_AMAC_DMSO_ADA WELL E4: 0.1M ADA/NAOH PH6.8, 12.0% W/V PEG 4,000, 0.25M AMMONIUM ACETATE, AND CRYO-PROTECTED IN 40% MPD WITH 0.1MM OF EACH COMPOUND; CRYSTAL TRACKING ID 249555E4 (BUV9-3), 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: 0.97872 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Oct 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→49.09 Å / Num. obs: 38978 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9 % / Biso Wilson estimate: 56.44 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 22.82 |
Reflection shell | Resolution: 2.5→2.56 Å / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 4.6 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→49.09 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.938 / SU B: 17.742 / SU ML: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.526 / ESU R Free: 0.255 Details: U VALUES : WITH TLS ADDED 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.1 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→49.09 Å
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