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Yorodumi- PDB-5ez7: Crystal structure of the FAD dependent oxidoreductase PA4991 from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ez7 | |||||||||
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Title | Crystal structure of the FAD dependent oxidoreductase PA4991 from Pseudomonas aeruginosa | |||||||||
Components | flavoenzyme PA4991 | |||||||||
Keywords | OXIDOREDUCTASE / flavoenzyme / flavine | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | |||||||||
Authors | Jacewicz, A. / Schnell, R. / Lindqvist, Y. / Schneider, G. | |||||||||
Funding support | Sweden, 2items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2016 Title: Crystal structure of the flavoenzyme PA4991 from Pseudomonas aeruginosa. Authors: Jacewicz, A. / Schnell, R. / Lindqvist, Y. / Schneider, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ez7.cif.gz | 155.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ez7.ent.gz | 120.5 KB | Display | PDB format |
PDBx/mmJSON format | 5ez7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ez7_validation.pdf.gz | 696.1 KB | Display | wwPDB validaton report |
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Full document | 5ez7_full_validation.pdf.gz | 699.6 KB | Display | |
Data in XML | 5ez7_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 5ez7_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/5ez7 ftp://data.pdbj.org/pub/pdb/validation_reports/ez/5ez7 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 42251.367 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: PA4991 / Plasmid: pNIC28Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HUH4 | ||
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#2: Chemical | ChemComp-FAD / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2 M trimethylamine N-oxide, 20% PEG2000 monomethyl-ether, 0.1 M Tris-HCl pH 8.5 PH range: 8.0-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.0093 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 12, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0093 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→61.32 Å / Num. obs: 14372 / % possible obs: 99.8 % / Redundancy: 7.4 % / Biso Wilson estimate: 41.2 Å2 / Rsym value: 0.072 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 5.3 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: ab initio model from Rosetta Resolution: 2.4→48.6 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.916 / SU B: 15.339 / SU ML: 0.185 / Cross valid method: THROUGHOUT / ESU R: 0.486 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.865 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→48.6 Å
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Refine LS restraints |
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