+Open data
-Basic information
Entry | Database: PDB / ID: 7qxr | ||||||
---|---|---|---|---|---|---|---|
Title | Azacoelenterazine-bound Renilla-type luciferase (AncFT) | ||||||
Components | Fragment transplantation onto a hyperstable ancestor of haloalkane dehalogenases and Renilla luciferase (Anc-FT) | ||||||
Keywords | OXIDOREDUCTASE / luciferase / azacoelenterazine / substrate analogue / Renilla-like / engineered ancestor | ||||||
Function / homology | Chem-NSW Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.052 Å | ||||||
Authors | Marek, M. / Schenkmayerova, A. / Janin, Y.L. | ||||||
Funding support | Czech Republic, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7qxr.cif.gz | 194.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7qxr.ent.gz | 154.8 KB | Display | PDB format |
PDBx/mmJSON format | 7qxr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qxr_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7qxr_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7qxr_validation.xml.gz | 35 KB | Display | |
Data in CIF | 7qxr_validation.cif.gz | 49.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qx/7qxr ftp://data.pdbj.org/pub/pdb/validation_reports/qx/7qxr | HTTPS FTP |
-Related structure data
Related structure data | 7omdC 7omoC 7omrC 7qxqC 6s97S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 33978.387 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.68 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: magnesium chloride, Bis-tris, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 12, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→46.944 Å / Num. obs: 56440 / % possible obs: 99.5 % / Redundancy: 6.9 % / CC1/2: 0.997 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.05→2.11 Å / Num. unique obs: 4304 / CC1/2: 0.591 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6S97 Resolution: 2.052→46.944 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.45 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.85 Å2 / Biso mean: 37.4412 Å2 / Biso min: 16.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.052→46.944 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|