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Yorodumi- PDB-8aq6: NanoLuc luciferase with bound furimamide in surface allosteric site -
+Open data
-Basic information
Entry | Database: PDB / ID: 8aq6 | ||||||
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Title | NanoLuc luciferase with bound furimamide in surface allosteric site | ||||||
Components | NanoLuc luciferase | ||||||
Keywords | LUMINESCENT PROTEIN / Luciferase / NanoLuc / NLuc / luciferin / furimazine | ||||||
Function / homology | Oplophorus-luciferin 2-monooxygenase / Oplophorus-luciferin 2-monooxygenase activity / bioluminescence / Calycin / extracellular region / Chem-NT0 / OXYGEN MOLECULE / TRIETHYLENE GLYCOL / Oplophorus-luciferin 2-monooxygenase catalytic subunit Function and homology information | ||||||
Biological species | Oplophorus gracilirostris (crustacean) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.69 Å | ||||||
Authors | Nemergut, M. / Marek, M. | ||||||
Funding support | Czech Republic, 1items
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Citation | Journal: Nat Commun / Year: 2023 Title: Illuminating the mechanism and allosteric behavior of NanoLuc luciferase. Authors: Nemergut, M. / Pluskal, D. / Horackova, J. / Sustrova, T. / Tulis, J. / Barta, T. / Baatallah, R. / Gagnot, G. / Novakova, V. / Majerova, M. / Sedlackova, K. / Marques, S.M. / Toul, M. / ...Authors: Nemergut, M. / Pluskal, D. / Horackova, J. / Sustrova, T. / Tulis, J. / Barta, T. / Baatallah, R. / Gagnot, G. / Novakova, V. / Majerova, M. / Sedlackova, K. / Marques, S.M. / Toul, M. / Damborsky, J. / Prokop, Z. / Bednar, D. / Janin, Y.L. / Marek, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8aq6.cif.gz | 595.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8aq6.ent.gz | 489.8 KB | Display | PDB format |
PDBx/mmJSON format | 8aq6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8aq6_validation.pdf.gz | 9.5 MB | Display | wwPDB validaton report |
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Full document | 8aq6_full_validation.pdf.gz | 9.5 MB | Display | |
Data in XML | 8aq6_validation.xml.gz | 66.2 KB | Display | |
Data in CIF | 8aq6_validation.cif.gz | 91 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/8aq6 ftp://data.pdbj.org/pub/pdb/validation_reports/aq/8aq6 | HTTPS FTP |
-Related structure data
Related structure data | 8aqhC 8aqiC 8bo9C 5b0uS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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8 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 20389.240 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oplophorus gracilirostris (crustacean) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q9GV45, Oplophorus-luciferin 2-monooxygenase |
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-Non-polymers , 7 types, 804 molecules
#2: Chemical | #3: Chemical | ChemComp-PG4 / #4: Chemical | ChemComp-OXY / | #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-PGE / | #7: Chemical | ChemComp-NT0 / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.23 Å3/Da / Density % sol: 44.96 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 200 mM MgCl2, 100 mM KCl, 25 mM Na acetate pH = 4.0, PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9999 Å | |||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 14, 2021 | |||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9999 Å / Relative weight: 1 | |||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.69→47.94 Å / Num. obs: 158483 / % possible obs: 99.3 % / Redundancy: 3.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.066 / Net I/σ(I): 9.7 | |||||||||||||||||||||||||
Reflection shell | Resolution: 1.69→1.73 Å / Num. unique obs: 14059 / CC1/2: 0.503 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5B0U Resolution: 1.69→47.94 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.232 / SU ML: 0.052 / SU R Cruickshank DPI: 0.0258 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.026 / ESU R Free: 0.019 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 169.07 Å2 / Biso mean: 31.334 Å2 / Biso min: 13.96 Å2
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Refinement step | Cycle: final / Resolution: 1.69→47.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.69→1.733 Å / Rfactor Rfree error: 0
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