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Yorodumi- PDB-3nkt: Crystal Structure of Salicylate 1,2-dioxygenase from Pseudoaminob... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3nkt | ||||||
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Title | Crystal Structure of Salicylate 1,2-dioxygenase from Pseudoaminobacter salicylatoxidans Adducts with naphthoate | ||||||
Components | Gentisate 1,2-Dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / BETA-SANDWICH | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudaminobacter salicylatoxidans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.35 Å | ||||||
Authors | Ferraroni, M. / Briganti, F. / Matera, I. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2012 Title: Crystal structures of salicylate 1,2-dioxygenase-substrates adducts: A step towards the comprehension of the structural basis for substrate selection in class III ring cleaving dioxygenases. Authors: Ferraroni, M. / Matera, I. / Steimer, L. / Burger, S. / Scozzafava, A. / Stolz, A. / Briganti, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nkt.cif.gz | 92.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nkt.ent.gz | 68.8 KB | Display | PDB format |
PDBx/mmJSON format | 3nkt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nkt_validation.pdf.gz | 451.3 KB | Display | wwPDB validaton report |
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Full document | 3nkt_full_validation.pdf.gz | 455.7 KB | Display | |
Data in XML | 3nkt_validation.xml.gz | 19.1 KB | Display | |
Data in CIF | 3nkt_validation.cif.gz | 28.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nk/3nkt ftp://data.pdbj.org/pub/pdb/validation_reports/nk/3nkt | HTTPS FTP |
-Related 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: 41144.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudaminobacter salicylatoxidans (bacteria) Strain: BN12 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q67FT0, gentisate 1,2-dioxygenase | ||
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#2: Chemical | ChemComp-FE2 / | ||
#3: Chemical | ChemComp-1HN / | ||
#4: Chemical | #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: 3.33 Å3/Da / Density % sol: 63.02 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 8 Details: 8% PEG10000, pH 8.0, vapor diffusion, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2009 |
Radiation | Monochromator: Si (111), horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8123 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→46.7 Å / Num. all: 21895 / Num. obs: 21895 / % possible obs: 94.7 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.47 / Rsym value: 0.44 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.35→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.201 / WRfactor Rwork: 0.1531 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8471 / SU B: 6.259 / SU ML: 0.15 / SU R Cruickshank DPI: 0.2667 / SU Rfree: 0.2232 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.223 / 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: 74.22 Å2 / Biso mean: 38.9106 Å2 / Biso min: 11.59 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.411 Å / Total num. of bins used: 20
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