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Yorodumi- PDB-3b9o: long-chain alkane monooxygenase (LadA) in complex with coenzyme FMN -
+Open data
-Basic information
Entry | Database: PDB / ID: 3b9o | ||||||
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Title | long-chain alkane monooxygenase (LadA) in complex with coenzyme FMN | ||||||
Components | Alkane monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / Geobacillus thermodenitrificans / LadA / alkane hydroxylase / monooxygenase / Plasmid | ||||||
Function / homology | Function and homology information long-chain alkane monooxygenase / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / nucleotide binding / extracellular region Similarity search - Function | ||||||
Biological species | Geobacillus thermodenitrificans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Li, L. / Yang, W. / Xu, F. / Bartlam, M. / Rao, Z. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Crystal structure of long-chain alkane monooxygenase (LadA) in complex with coenzyme FMN: unveiling the long-chain alkane hydroxylase Authors: Li, L. / Liu, X. / Yang, W. / Xu, F. / Wang, W. / Feng, L. / Bartlam, M. / Wang, L. / Rao, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3b9o.cif.gz | 190.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3b9o.ent.gz | 151.7 KB | Display | PDB format |
PDBx/mmJSON format | 3b9o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3b9o_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 3b9o_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 3b9o_validation.xml.gz | 38 KB | Display | |
Data in CIF | 3b9o_validation.cif.gz | 53.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/3b9o ftp://data.pdbj.org/pub/pdb/validation_reports/b9/3b9o | HTTPS FTP |
-Related structure data
Related structure data | 3b9nSC 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 50540.121 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus thermodenitrificans (bacteria) Gene: ladA / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: A4IU28, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced iron-sulfur protein as one donor, and incorporation of one ...References: UniProt: A4IU28, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced iron-sulfur protein as one donor, and incorporation of one atom of oxygen into the other donor #2: Chemical | #3: 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: 2.37 Å3/Da / Density % sol: 48.07 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M ADA pH 6.5, 0.2mM Ammonium acetate, 40-43% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9793 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. obs: 90836 / Redundancy: 6.4 % / Rmerge(I) obs: 0.088 |
Reflection shell | Resolution: 1.86→1.94 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.088 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3B9N Resolution: 1.9→50 Å / Cross valid method: THROUGHOUT / Details: REFMAC 5.0 was also used for the refinement
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Refinement step | Cycle: LAST / Resolution: 1.9→50 Å
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Refine LS restraints |
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