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- PDB-7omo: Crystal structure of coelenteramine-bound Renilla reniformis luci... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7omo | ||||||
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Title | Crystal structure of coelenteramine-bound Renilla reniformis luciferase RLuc8-D120A variant | ||||||
![]() | Renilla reniformis luciferase RLuc8-D120A variant | ||||||
![]() | LUMINESCENT PROTEIN / bioluminscence / coelenteramide-bound enzyme | ||||||
Function / homology | 4-[5-azanyl-6-(phenylmethyl)pyrazin-2-yl]phenol![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Schenkmayerova, A. / Marek, M. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 147.4 KB | Display | ![]() |
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PDB format | ![]() | 115 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.7 MB | Display | ![]() |
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Full document | ![]() | 2.7 MB | Display | |
Data in XML | ![]() | 27.1 KB | Display | |
Data in CIF | ![]() | 40.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7omdC ![]() 7omrC ![]() 7qxqC ![]() 7qxrC ![]() 2spjS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 472 molecules ![](data/chem/img/VKB.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-VKB / | ||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 43.74 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG3350, magnesium chloride, bis-tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 27, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.45→46.751 Å / Num. obs: 111521 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 17.13 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.019 / Rrim(I) all: 0.049 / Net I/σ(I): 21.2 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2SPJ Resolution: 1.451→46.751 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.54 / 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: 72.98 Å2 / Biso mean: 22.9199 Å2 / Biso min: 10.4 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.451→46.751 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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