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Yorodumi- PDB-6ac3: Structure of a natural red emitting luciferase from Phrixothrix h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ac3 | ||||||
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Title | Structure of a natural red emitting luciferase from Phrixothrix hirtus (P3121 crystal form) | ||||||
Components | Red-bioluminescence eliciting luciferase | ||||||
Keywords | LUMINESCENT PROTEIN / bioluminescence / Luciferase / Red emission | ||||||
Function / homology | Function and homology information firefly luciferase / monooxygenase activity / bioluminescence / peroxisome Similarity search - Function | ||||||
Biological species | Phrixothrix hirtus (beetle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å | ||||||
Authors | Carrasco-Lopez, C. / Panjikar, S. / Naumov, P. / Rabeh, W. | ||||||
Funding support | United Arab Emirates, 1items
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Citation | Journal: Life Sci Alliance / Year: 2018 Title: Beetle luciferases with naturally red- and blue-shifted emission. Authors: Carrasco-Lopez, C. / Ferreira, J.C. / Lui, N.M. / Schramm, S. / Berraud-Pache, R. / Navizet, I. / Panjikar, S. / Naumov, P. / Rabeh, W.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ac3.cif.gz | 354 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ac3.ent.gz | 287.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ac3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ac3_validation.pdf.gz | 478 KB | Display | wwPDB validaton report |
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Full document | 6ac3_full_validation.pdf.gz | 558.6 KB | Display | |
Data in XML | 6ac3_validation.xml.gz | 70 KB | Display | |
Data in CIF | 6ac3_validation.cif.gz | 93.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ac/6ac3 ftp://data.pdbj.org/pub/pdb/validation_reports/ac/6ac3 | HTTPS FTP |
-Related structure data
Related structure data | 6aaaSC 6abhC 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: 60833.215 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phrixothrix hirtus (beetle) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9U4U7 |
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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: 2.96 Å3/Da / Density % sol: 58.4 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 19 to 21% PEG 3350, 0.1M Bis-tris propane, pH 6.0 supplemented with 0.2M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→19.85 Å / Num. obs: 33877 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / CC1/2: 0.985 / Rmerge(I) obs: 0.211 / Rpim(I) all: 0.144 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 3.6→3.78 Å / Rmerge(I) obs: 0.936 / CC1/2: 0.504 / Rpim(I) all: 0.633 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6AAA Resolution: 3.6→19.85 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.51 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.6→19.85 Å
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Refine LS restraints |
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LS refinement shell |
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