+Open data
-Basic information
Entry | Database: PDB / ID: 8cbb | ||||||
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Title | Structure of homodimeric luciferase from Enhygromyxa salina | ||||||
Components | Alkanal monooxygenase alpha chain | ||||||
Keywords | LUMINESCENT PROTEIN / Luciferase / monooxygenase | ||||||
Function / homology | bacterial luciferase / alkanal monooxygenase (FMN-linked) activity / Bacterial luciferase/NFP / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / bacterial luciferase Function and homology information | ||||||
Biological species | Enhygromyxa salina (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å | ||||||
Authors | Yudenko, A. / Remeeva, A. / Gushchin, I. | ||||||
Funding support | Russian Federation, 1items
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Citation | Journal: To Be Published Title: Structure of homodimeric luciferase from Enhygromyxa salina Authors: Yudenko, A. / Remeeva, A. / Gushchin, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cbb.cif.gz | 278.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cbb.ent.gz | 224.3 KB | Display | PDB format |
PDBx/mmJSON format | 8cbb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cbb_validation.pdf.gz | 472.6 KB | Display | wwPDB validaton report |
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Full document | 8cbb_full_validation.pdf.gz | 492.6 KB | Display | |
Data in XML | 8cbb_validation.xml.gz | 49.7 KB | Display | |
Data in CIF | 8cbb_validation.cif.gz | 67.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/8cbb ftp://data.pdbj.org/pub/pdb/validation_reports/cb/8cbb | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 42276.000 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enhygromyxa salina (bacteria) / Gene: luxA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S9XZH0 #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.22 Å3/Da / Density % sol: 44.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: PEG3350 25%, lithium sulfate 0.2 M, BIS-TRIS 0.1 M pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762 Å |
Detector | Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Oct 11, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 2.71→91.89 Å / Num. obs: 35543 / % possible obs: 97 % / Redundancy: 1.8 % / CC1/2: 0.981 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.068 / Rrim(I) all: 0.096 / Χ2: 0.35 / Net I/σ(I): 4 / Num. measured all: 63062 |
Reflection shell | Resolution: 2.71→2.84 Å / % possible obs: 96.2 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.218 / Num. measured all: 8436 / Num. unique obs: 4681 / CC1/2: 0.894 / Rpim(I) all: 0.218 / Rrim(I) all: 0.308 / Χ2: 0.42 / Net I/σ(I) obs: 2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→91.89 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.87 / SU B: 18.929 / SU ML: 0.367 / Cross valid method: THROUGHOUT / ESU R Free: 0.429 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.378 Å2
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Refinement step | Cycle: 1 / Resolution: 2.71→91.89 Å
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