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Yorodumi- PDB-6bka: Crystal Structure of Nitronate Monooxygenase from Cyberlindnera s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6bka | ||||||
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Title | Crystal Structure of Nitronate Monooxygenase from Cyberlindnera saturnus | ||||||
Components | Nitronate monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / Monooxygenase / Propionate 3-nitronate | ||||||
Function / homology | nitronate monooxygenase / nitronate monooxygenase activity / Nitronate monooxygenase / Nitronate monooxygenase / Aldolase-type TIM barrel / Chem-33O / FLAVIN MONONUCLEOTIDE / Nitronate monooxygenase Function and homology information | ||||||
Biological species | Cyberlindnera mrakii (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Agniswamy, J. / Fang, Y.-F. / Weber, I.T. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proteins / Year: 2018 Title: Crystal structure of yeast nitronate monooxygenase from Cyberlindnera saturnus. Authors: Agniswamy, J. / Reis, R.A.G. / Wang, Y.F. / Smitherman, C. / Su, D. / Weber, I. / Gadda, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bka.cif.gz | 102.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bka.ent.gz | 74.9 KB | Display | PDB format |
PDBx/mmJSON format | 6bka.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bka_validation.pdf.gz | 955.4 KB | Display | wwPDB validaton report |
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Full document | 6bka_full_validation.pdf.gz | 967.5 KB | Display | |
Data in XML | 6bka_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 6bka_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/6bka ftp://data.pdbj.org/pub/pdb/validation_reports/bk/6bka | HTTPS FTP |
-Related structure data
Related structure data | 4q4kS S: Starting model for refinement |
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Similar 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: 41545.988 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cyberlindnera mrakii (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q12723, nitronate monooxygenase |
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#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-33O / |
#4: Chemical | ChemComp-GOL / |
#5: 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: 2.07 Å3/Da / Density % sol: 40.51 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 21% PEG 3350, 70 mM Sodium Citrate at pH 4.0 and 100 mM Ammonium Acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 27, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. obs: 39464 / % possible obs: 96 % / Redundancy: 5 % / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.037 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2967 / CC1/2: 0.782 / Χ2: 1.08 / % possible all: 72.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Q4K Resolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.808 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.092 / 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: 18.707 Å2
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Refinement step | Cycle: 1 / Resolution: 1.65→50 Å
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Refine LS restraints |
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