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Yorodumi- PDB-5hm3: 2.25 Angstrom Resolution Crystal Structure of Long-chain-fatty-ac... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hm3 | ||||||
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Title | 2.25 Angstrom Resolution Crystal Structure of Long-chain-fatty-acid-AMP Ligase FadD32 from Mycobacterium tuberculosis in complex with Inhibitor 5'-O-[(11-phenoxyundecanoyl)sulfamoyl]adenosine | ||||||
Components | Long-chain-fatty-acid--AMP ligase FadD32 | ||||||
Keywords | LIGASE/LIGASE INHIBITOR / long-chain-fatty-acid--AMP ligase / FadD32 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / LIGASE-LIGASE INHIBITOR complex | ||||||
Function / homology | Function and homology information long-chain-fatty-acid-[acyl-carrier-protein] ligase / long-chain fatty acid [acyl-carrier-protein] ligase activity / adenylyltransferase activity / Actinobacterium-type cell wall biogenesis / mycolate cell wall layer assembly / cell wall / lipid biosynthetic process / ligase activity / fatty acid biosynthetic process / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å | ||||||
Authors | Minasov, G. / Warwrzak, Z. / Kuhn, M.L. / Shuvalova, L. / Flores, K.J. / Wilson, D.J. / Grimes, K.D. / Aldrich, C.C. / Anderson, W.A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: Acs Infect Dis. / Year: 2016 Title: Structure of the Essential Mtb FadD32 Enzyme: A Promising Drug Target for Treating Tuberculosis. Authors: Kuhn, M.L. / Alexander, E. / Minasov, G. / Page, H.J. / Warwrzak, Z. / Shuvalova, L. / Flores, K.J. / Wilson, D.J. / Shi, C. / Aldrich, C.C. / Anderson, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hm3.cif.gz | 268.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hm3.ent.gz | 224.3 KB | Display | PDB format |
PDBx/mmJSON format | 5hm3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/5hm3 ftp://data.pdbj.org/pub/pdb/validation_reports/hm/5hm3 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 71887.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: fadD32, Rv3801c / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O53580, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases |
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-Non-polymers , 6 types, 140 molecules
#2: Chemical | ChemComp-649 / | ||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-PEG / | #6: Chemical | #7: 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: 2.02 Å3/Da / Density % sol: 39 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: Protein: 6.0 mG/mL, 0.1M Pottasium chloride, 0.01 M Tris-HCL buffer pH 8.3, 5% glycerol, and 0.5 mM TCEP; Screen: Cubic Phase I (F10), 2.4 M Na/K phosphate pH 7.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97875 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 20, 2014 / Details: Si(111) |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97875 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→30 Å / Num. obs: 29261 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 49.5 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 2.25→2.29 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 2.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.25→29.36 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / SU B: 13.796 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.376 / ESU R Free: 0.238 / Details: 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: 62.991 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→29.36 Å
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