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Yorodumi- PDB-7omd: Crystal structure of azacoelenterazine-bound Renilla reniformis l... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7omd | ||||||
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Title | Crystal structure of azacoelenterazine-bound Renilla reniformis luciferase variant RLuc8-D162A | ||||||
Components | Coelenterazine h 2-monooxygenase | ||||||
Keywords | LUMINESCENT PROTEIN / bioluminscence | ||||||
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: 1.601 Å | ||||||
Authors | Schenkmayerova, A. / Janin, Y.L. / Marek, M. | ||||||
Funding support | Czech Republic, 1items
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Citation | Journal: Nat Catal / Year: 2023 Title: Catalytic mechanism for Renilla-type luciferases Authors: Schenkmayerova, A. / Toul, M. / Pluskal, D. / Baatallah, R. / Gagnot, G. / Pinto, G.P. / Santana, V.T. / Stuchla, M. / Neugebauer, P. / Chaiyen, P. / Damborsky, J. / Bednar, D. / Janin, Y.L. ...Authors: Schenkmayerova, A. / Toul, M. / Pluskal, D. / Baatallah, R. / Gagnot, G. / Pinto, G.P. / Santana, V.T. / Stuchla, M. / Neugebauer, P. / Chaiyen, P. / Damborsky, J. / Bednar, D. / Janin, Y.L. / Prokop, Z. / Marek, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7omd.cif.gz | 301.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7omd.ent.gz | 244.7 KB | Display | PDB format |
PDBx/mmJSON format | 7omd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/om/7omd ftp://data.pdbj.org/pub/pdb/validation_reports/om/7omd | HTTPS FTP |
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-Related structure data
Related structure data | 7omoC 7omrC 7qxqC 7qxrC 2psjS 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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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: 36903.164 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, 697 molecules
#2: Chemical | ChemComp-VK8 / #3: Chemical | ChemComp-DMS / | #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-CL / | #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: 2 Å3/Da / Density % sol: 45.91 % |
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Crystal grow | Temperature: 293.5 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG3350, Bis-tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å | |||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 4, 2019 | |||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 1.6→43.95 Å / Num. obs: 86744 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.023 / Rrim(I) all: 0.059 / Net I/σ(I): 20 / Num. measured all: 585268 / Scaling rejects: 36 | |||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 6.4 %
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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: 1.601→38.401 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.91 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 111.61 Å2 / Biso mean: 28.8524 Å2 / Biso min: 12.33 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.601→38.401 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Origin x: 11.925 Å / Origin y: -5.64 Å / Origin z: 18.453 Å
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Refinement TLS group |
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