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Yorodumi- PDB-6yn2: Crystal structure of Renilla reniformis luciferase variant RLuc8-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yn2 | ||||||
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Title | Crystal structure of Renilla reniformis luciferase variant RLuc8-W121F/E144Q in complex with a coelenteramide (the postcatalytic enzyme-product complex) | ||||||
Components | Coelenterazine h 2-monooxygenase | ||||||
Keywords | LUMINESCENT PROTEIN / bioluminscence / coelenteramide-bound enzyme | ||||||
Function / homology | Function and homology information Renilla-type luciferase / Renilla-luciferin 2-monooxygenase activity / carboxy-lyase activity / bioluminescence Similarity search - Function | ||||||
Biological species | Renilla reniformis (sea pansy) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Authors | Damborsky, J. / Marek, M. | ||||||
Funding support | Czech Republic, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Engineering the protein dynamics of an ancestral luciferase. Authors: Schenkmayerova, A. / Pinto, G.P. / Toul, M. / Marek, M. / Hernychova, L. / Planas-Iglesias, J. / Daniel Liskova, V. / Pluskal, D. / Vasina, M. / Emond, S. / Dorr, M. / Chaloupkova, R. / ...Authors: Schenkmayerova, A. / Pinto, G.P. / Toul, M. / Marek, M. / Hernychova, L. / Planas-Iglesias, J. / Daniel Liskova, V. / Pluskal, D. / Vasina, M. / Emond, S. / Dorr, M. / Chaloupkova, R. / Bednar, D. / Prokop, Z. / Hollfelder, F. / Bornscheuer, U.T. / Damborsky, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yn2.cif.gz | 152.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yn2.ent.gz | 117.8 KB | Display | PDB format |
PDBx/mmJSON format | 6yn2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/6yn2 ftp://data.pdbj.org/pub/pdb/validation_reports/yn/6yn2 | HTTPS FTP |
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-Related structure data
Related structure data | 6s6eC 6s97C 2psjS 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 36907.156 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Renilla reniformis (sea pansy) / Production host: Escherichia coli (E. coli) / References: UniProt: P27652, Renilla-type luciferase |
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-Non-polymers , 5 types, 512 molecules
#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-K / | #6: 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: 3.56 Å3/Da / Density % sol: 65.4 % |
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Crystal grow | Temperature: 293.5 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: NaHPO4/K2HPO4, sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99987 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 7, 2019 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.99987 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.9→48.66 Å / Num. obs: 82701 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.032 / Rrim(I) all: 0.119 / Net I/σ(I): 18.5 / Num. measured all: 1120338 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PSJ Resolution: 1.9→44.528 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.03
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 86.2 Å2 / Biso mean: 34.5373 Å2 / Biso min: 19.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→44.528 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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