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Yorodumi- PDB-3kg1: Crystal structure of SnoaB, a cofactor-independent oxygenase from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kg1 | ||||||
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Title | Crystal structure of SnoaB, a cofactor-independent oxygenase from Streptomyces nogalater, mutant N63A | ||||||
Components | SnoaB | ||||||
Keywords | OXIDOREDUCTASE / polyketide / anthracycline / oxygenase / cofactor-independent | ||||||
Function / homology | Function and homology information deoxynogalonate monooxygenase / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of one atom of oxygen (internal monooxygenases or internal mixed function oxidases) / antibiotic biosynthetic process Similarity search - Function | ||||||
Biological species | Streptomyces nogalater (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å | ||||||
Authors | Koskiniemi, H. / Grocholski, T. / Lindqvist, Y. / Mantsala, P. / Niemi, J. / Schneider, G. | ||||||
Citation | Journal: Biochemistry / Year: 2010 Title: Crystal structure of the cofactor-independent monooxygenase SnoaB from Streptomyces nogalater: implications for the reaction mechanism Authors: Grocholski, T. / Koskiniemi, H. / Lindqvist, Y. / Mantsala, P. / Niemi, J. / Schneider, G. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Expression, purification and crystallization of the cofactor-independent monooxygenase SnoaB from the nogalamycin biosynthetic pathway Authors: Koskiniemi, H. / Grocholski, T. / Schneider, G. / Niemi, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kg1.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kg1.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 3kg1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kg/3kg1 ftp://data.pdbj.org/pub/pdb/validation_reports/kg/3kg1 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 4
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-Components
#1: Protein | Mass: 14311.804 Da / Num. of mol.: 3 / Fragment: oxygenase / Mutation: N63A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces nogalater (bacteria) / Gene: SnoaB / Plasmid: modified from pBAD/HisB / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: O54259 #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | AUTHORS STATE THAT G25A IS IN FACT THE NATIVE SEQUENCE. THEY CONFIRMED THEIR NATIVE SEQUENCE BY DNA- ...AUTHORS STATE THAT G25A IS IN FACT THE NATIVE SEQUENCE. THEY CONFIRMED THEIR NATIVE SEQUENCE BY DNA-SEQUENCING | |
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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: 1.98 Å3/Da / Density % sol: 31.94 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PEG MME 2K, KBr, pentaerythritol ethoxylate , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 12, 2009 |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30 Å / Num. all: 11301 / Num. obs: 11301 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 52.5 Å2 / Rsym value: 0.103 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2 / Num. unique all: 1591 / Rsym value: 0.571 / % possible all: 99.3 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→29.42 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.904 / Occupancy max: 1 / Occupancy min: 0 / SU B: 25.621 / SU ML: 0.261 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.71 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 70.71 Å2 / Biso mean: 35.709 Å2 / Biso min: 17.85 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→29.42 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 1100 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.5→2.564 Å / Total num. of bins used: 20
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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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