+Open data
-Basic information
Entry | Database: PDB / ID: 3l66 | ||||||
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Title | Xenobiotic Reductase A - C25A Variant with Coumarin | ||||||
Components | Xenobiotic reductase A | ||||||
Keywords | OXIDOREDUCTASE / FMN / flavin / old-yellow-enzyme | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.28 Å | ||||||
Authors | Spiegelhauer, O. / Dobbek, H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Cysteine as a modulator residue in the active site of xenobiotic reductase A: a structural, thermodynamic and kinetic study Authors: Spiegelhauer, O. / Mende, S. / Dickert, F. / Knauer, S.H. / Ullmann, G.M. / Dobbek, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l66.cif.gz | 327 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l66.ent.gz | 264.6 KB | Display | PDB format |
PDBx/mmJSON format | 3l66.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3l66_validation.pdf.gz | 851.1 KB | Display | wwPDB validaton report |
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Full document | 3l66_full_validation.pdf.gz | 856 KB | Display | |
Data in XML | 3l66_validation.xml.gz | 23 KB | Display | |
Data in CIF | 3l66_validation.cif.gz | 36.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l6/3l66 ftp://data.pdbj.org/pub/pdb/validation_reports/l6/3l66 | HTTPS FTP |
-Related structure data
Related structure data | 3l5lC 3l5mC 3l65SC 3l67C 3l68C C: citing same article (ref.) 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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39881.953 Da / Num. of mol.: 1 / Mutation: C25A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: 86 / Gene: xenA / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q3ZDM6*PLUS, NADPH dehydrogenase |
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-Non-polymers , 5 types, 643 molecules
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-FMN / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | A SEQUENCE DATABASE REFERENCE WHICH DERIVES FROM PSEUDOMONAS PUTIDA STRAIN 86 DOES NOT CURRENTLY ...A SEQUENCE DATABASE REFERENCE WHICH DERIVES FROM PSEUDOMONA |
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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: 2.38 Å3/Da / Density % sol: 48.31 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.5M Ammonium sulfate, 100mM Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.92 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→33.11 Å / Num. all: 98065 / Num. obs: 96595 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 8.88 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3L65 Resolution: 1.28→33.11 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.915 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 15 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.885 Å2 / ksol: 0.36 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 420.95 Å2 / Biso mean: 18.878 Å2 / Biso min: 4.88 Å2
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Refinement step | Cycle: LAST / Resolution: 1.28→33.11 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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