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Yorodumi- PDB-4f6l: Crystal structure of Aureusimine biosynthetic cluster reductase domain -
+Open data
-Basic information
Entry | Database: PDB / ID: 4f6l | ||||||
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Title | Crystal structure of Aureusimine biosynthetic cluster reductase domain | ||||||
Components | AusA reductase domain protein | ||||||
Keywords | OXIDOREDUCTASE / Thioester reductase | ||||||
Function / homology | Function and homology information : / organonitrogen compound biosynthetic process / acyltransferase activity / catalytic activity / fatty acid metabolic process / oxidoreductase activity Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.856 Å | ||||||
Authors | Mok, M. / Junop, M. | ||||||
Citation | Journal: Chembiochem / Year: 2012 Title: Heterologous expression and structural characterisation of a pyrazinone natural product assembly line. Authors: Wyatt, M.A. / Mok, M.C. / Junop, M. / Magarvey, N.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f6l.cif.gz | 307.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f6l.ent.gz | 251 KB | Display | PDB format |
PDBx/mmJSON format | 4f6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/4f6l ftp://data.pdbj.org/pub/pdb/validation_reports/f6/4f6l | HTTPS FTP |
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-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
#1: Protein | Mass: 58070.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / ATCC 700699 / Gene: SAV0179 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99X42, UniProt: A0A0H3JX00*PLUS |
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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: 3.1 Å3/Da / Density % sol: 60.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 10% (w/v) PEG8000, 0.1 M Tris pH 7, 0.2 M MgCl2., VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2011 |
Radiation | Monochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3.856→50 Å / Num. all: 13944 / Num. obs: 13944 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 3.9→3.97 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.856→49.626 Å / SU ML: 1.18 / σ(F): 1.35 / Phase error: 23.73 / 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: 104.886 Å2 / ksol: 0.335 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 3.856→49.626 Å
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Refine LS restraints |
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LS refinement shell |
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