+Open data
-Basic information
Entry | Database: PDB / ID: 6fri | ||||||
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Title | Structure of LuxB from Photobacterium leiognathi | ||||||
Components | Alkanal monooxygenase beta chain | ||||||
Keywords | OXIDOREDUCTASE / LUCIFERASE / MONO-OXYGENASE / BETA-DIMER / bioluminescence | ||||||
Function / homology | Function and homology information bacterial luciferase / alkanal monooxygenase (FMN-linked) activity / bioluminescence Similarity search - Function | ||||||
Biological species | Photobacterium leiognathi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.297 Å | ||||||
Authors | Uhl, M. / Gruber, K. | ||||||
Funding support | Austria, 1items
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Citation | Journal: to be published Title: Structure of LuxB from Photobacterium leiognathi Authors: Uhl, M. / Gruber, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fri.cif.gz | 273 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fri.ent.gz | 220.9 KB | Display | PDB format |
PDBx/mmJSON format | 6fri.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fri_validation.pdf.gz | 454.5 KB | Display | wwPDB validaton report |
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Full document | 6fri_full_validation.pdf.gz | 459.6 KB | Display | |
Data in XML | 6fri_validation.xml.gz | 48.4 KB | Display | |
Data in CIF | 6fri_validation.cif.gz | 68.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/6fri ftp://data.pdbj.org/pub/pdb/validation_reports/fr/6fri | HTTPS FTP |
-Related structure data
Related structure data | 3fgcS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 37395.156 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photobacterium leiognathi (bacteria) / Gene: luxB / Production host: Escherichia coli (E. coli) / References: UniProt: P09141, bacterial luciferase #2: Chemical | ChemComp-ACT / | #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: 2.38 Å3/Da / Density % sol: 48.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M BisTris pH 5 40 mM NH4 Acetate 40% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 1 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Oct 8, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→42 Å / Num. obs: 60104 / % possible obs: 95.1 % / Redundancy: 3.1 % / CC1/2: 0.985 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.103 / Net I/σ(I): 19.45 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.696 / CC1/2: 0.657 / Rpim(I) all: 0.488 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3FGC Resolution: 2.297→42.089 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.26
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.297→42.089 Å
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Refine LS restraints |
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LS refinement shell |
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