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Yorodumi- PDB-5wgy: Crystal Structure of MalA' C112S/C128S, malbrancheamide B complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wgy | |||||||||||||||
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Title | Crystal Structure of MalA' C112S/C128S, malbrancheamide B complex | |||||||||||||||
Components | Flavin-dependent halogenase | |||||||||||||||
Keywords | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / flavin-dependent halogenase / malbrancheamide / zinc / Zn / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex | |||||||||||||||
Function / homology | Function and homology information flavin-dependent halogenase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / secondary metabolite biosynthetic process / monooxygenase activity Similarity search - Function | |||||||||||||||
Biological species | Malbranchea aurantiaca (fungus) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||||||||
Authors | Fraley, A.E. / Smith, J.L. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2017 Title: Function and Structure of MalA/MalA', Iterative Halogenases for Late-Stage C-H Functionalization of Indole Alkaloids. Authors: Fraley, A.E. / Garcia-Borras, M. / Tripathi, A. / Khare, D. / Mercado-Marin, E.V. / Tran, H. / Dan, Q. / Webb, G.P. / Watts, K.R. / Crews, P. / Sarpong, R. / Williams, R.M. / Smith, J.L. / ...Authors: Fraley, A.E. / Garcia-Borras, M. / Tripathi, A. / Khare, D. / Mercado-Marin, E.V. / Tran, H. / Dan, Q. / Webb, G.P. / Watts, K.R. / Crews, P. / Sarpong, R. / Williams, R.M. / Smith, J.L. / Houk, K.N. / Sherman, D.H. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wgy.cif.gz | 291.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wgy.ent.gz | 233.2 KB | Display | PDB format |
PDBx/mmJSON format | 5wgy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5wgy_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5wgy_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5wgy_validation.xml.gz | 30 KB | Display | |
Data in CIF | 5wgy_validation.cif.gz | 45.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/5wgy ftp://data.pdbj.org/pub/pdb/validation_reports/wg/5wgy | HTTPS FTP |
-Related structure data
Related structure data | 5wgrSC 5wgsC 5wgtC 5wguC 5wgvC 5wgwC 5wgxC 5wgzC S: Starting model for refinement C: citing same article (ref.) |
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Similar 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 74665.359 Da / Num. of mol.: 1 / Mutation: Cys112Ser, Cys128Ser, Leu276Pro, Arg428Pro Source method: isolated from a genetically manipulated source Source: (gene. exp.) Malbranchea aurantiaca (fungus) / Gene: malA / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: L0E155 |
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-Non-polymers , 7 types, 485 molecules
#2: Chemical | ChemComp-FAD / | ||||||||||
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#3: Chemical | #4: Chemical | ChemComp-ZN / | #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-CL / | #7: Chemical | #8: 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: 2.74 Å3/Da / Density % sol: 55.16 % / Mosaicity: 0.13 ° |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 2 M ammonium sulfate, 0.2 M lithium sulfate, 0.1 M Bis-Tris pH 5.5, 5 mM cadmium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 7, 2017 |
Radiation | Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 2→46.26 Å / Num. obs: 55523 / % possible obs: 99.88 % / Redundancy: 6.8 % / Biso Wilson estimate: 37.64 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07874 / Rpim(I) all: 0.034 / Rrim(I) all: 0.089 / Net I/σ(I): 15.97 |
Reflection shell | Resolution: 2→2.072 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.369 / Mean I/σ(I) obs: 1.41 / Num. unique obs: 5464 / CC1/2: 0.548 / Rpim(I) all: 0.604 / Rrim(I) all: 1.613 / % possible all: 99.76 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5WGR Resolution: 2→46.26 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.15
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 139.91 Å2 / Biso mean: 42.9992 Å2 / Biso min: 22.15 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→46.26 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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