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Yorodumi- PDB-3k88: Crystal structure of NADH:FAD oxidoreductase (TftC) - FAD, NADH c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k88 | ||||||
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Title | Crystal structure of NADH:FAD oxidoreductase (TftC) - FAD, NADH complex | ||||||
Components | Chlorophenol-4-monooxygenase component 1 | ||||||
Keywords | OXIDOREDUCTASE / NADH:FAD oxidoreductase / Monooxygenase | ||||||
Function / homology | Function and homology information FAD reductase (NADH) / oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor / pyrimidine nucleobase catabolic process / riboflavin reductase (NADPH) activity / : / monooxygenase activity / FMN binding / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Burkholderia cepacia (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kang, C. / Webb, B.N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Characterization of chlorophenol 4-monooxygenase (TftD) and NADH:FAD oxidoreductase (TftC) of Burkholderia cepacia AC1100. Authors: Webb, B.N. / Ballinger, J.W. / Kim, E. / Belchik, S.M. / Lam, K.S. / Youn, B. / Nissen, M.S. / Xun, L. / Kang, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k88.cif.gz | 88.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k88.ent.gz | 65.7 KB | Display | PDB format |
PDBx/mmJSON format | 3k88.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3k88_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 3k88_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 3k88_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 3k88_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k8/3k88 ftp://data.pdbj.org/pub/pdb/validation_reports/k8/3k88 | HTTPS FTP |
-Related structure data
Related structure data | 3hwcC 3k86SC 3k87C S: Starting model for refinement C: citing same article (ref.) |
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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: 19875.557 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cepacia (bacteria) / Strain: AC1100 / Gene: tftC / Plasmid: pET30 LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O87008 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 3.15 Å3/Da / Density % sol: 60.93 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M Potassium formate, 20% w/v PEG 4000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Details: Pt-coated Si |
Radiation | Monochromator: KOHZU: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→35.27 Å / Num. obs: 35903 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3K86 Resolution: 2→19.236 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.34 / 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: 58.963 Å2 / ksol: 0.386 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 111.53 Å2 / Biso mean: 31.772 Å2 / Biso min: 14.87 Å2
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Refinement step | Cycle: LAST / Resolution: 2→19.236 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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