+Open data
-Basic information
Entry | Database: PDB / ID: 4ir7 | ||||||
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Title | Crystal Structure of Mtb FadD10 in Complex with Dodecanoyl-AMP | ||||||
Components | Long chain fatty acid CoA ligase FadD10 | ||||||
Keywords | TRANSFERASE / open conformation / Structural Genomics / TB Structural Genomics Consortium / TBSGC | ||||||
Function / homology | ANL, C-terminal domain / ANL, N-terminal domain / GMP Synthetase; Chain A, domain 3 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta / Chem-1ZZ / : Function and homology information | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Liu, Z. / Wang, F. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC) | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: Structures of Mycobacterium tuberculosis FadD10 protein reveal a new type of adenylate-forming enzyme. Authors: Liu, Z. / Ioerger, T.R. / Wang, F. / Sacchettini, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ir7.cif.gz | 108.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ir7.ent.gz | 81.5 KB | Display | PDB format |
PDBx/mmJSON format | 4ir7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ir7_validation.pdf.gz | 698.7 KB | Display | wwPDB validaton report |
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Full document | 4ir7_full_validation.pdf.gz | 701.5 KB | Display | |
Data in XML | 4ir7_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 4ir7_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ir/4ir7 ftp://data.pdbj.org/pub/pdb/validation_reports/ir/4ir7 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 56727.488 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv0099 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) plys / References: UniProt: I6WXG2, fatty-acyl-CoA synthase system |
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#2: Chemical | ChemComp-1ZZ / |
#3: Chemical | ChemComp-MG / |
#4: 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: 4.01 Å3/Da / Density % sol: 69.36 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 6000, LiSO4, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 120 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.542 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 1, 2007 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→50 Å / Num. obs: 24707 / % possible obs: 99.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.109 / Χ2: 1.603 / Net I/σ(I): 6.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→39.034 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7788 / SU ML: 0.4 / σ(F): 1.34 / Phase error: 28.43 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.369 Å2 / ksol: 0.327 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 141.69 Å2 / Biso mean: 63.6413 Å2 / Biso min: 28.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→39.034 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8
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