+Open data
-Basic information
Entry | Database: PDB / ID: 8wvb | ||||||
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Title | Crystal structure of Lsd18 mutant S195M | ||||||
Components | Putative epoxidase LasC | ||||||
Keywords | FLAVOPROTEIN / FAD dependent monooxygenase / epoxidase / mutant | ||||||
Function / homology | Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor / FAD-binding domain / FAD binding domain / antibiotic biosynthetic process / monooxygenase activity / FAD binding / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / Putative epoxidase LasC Function and homology information | ||||||
Biological species | Streptomyces lasalocidi (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Liu, N. / Xiao, H.L. / Chen, X. | ||||||
Funding support | China, 1items
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Citation | Journal: Int J Mol Sci / Year: 2023 Title: Simultaneous Improvement in the Thermostability and Catalytic Activity of Epoxidase Lsd18 for the Synthesis of Lasalocid A. Authors: Liu, N. / Xiao, H. / Zang, Y. / Zhou, L. / Mencius, J. / Yang, Z. / Quan, S. / Chen, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wvb.cif.gz | 348.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wvb.ent.gz | 280.2 KB | Display | PDB format |
PDBx/mmJSON format | 8wvb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/8wvb ftp://data.pdbj.org/pub/pdb/validation_reports/wv/8wvb | HTTPS FTP |
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-Related structure data
Related structure data | 8wvfC 8up4 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
#1: Protein | Mass: 52690.812 Da / Num. of mol.: 2 / Mutation: S195M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces lasalocidi (bacteria) / Gene: lsd18 / Production host: Escherichia coli (E. coli) / References: UniProt: B5M9L6 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | 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: 2.03 Å3/Da / Density % sol: 39.32 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion Details: 0.2 M Ammonium acetate, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→30.114 Å / Num. obs: 28322 / % possible obs: 99.03 % / Redundancy: 6.7 % / CC1/2: 0.918 / Rmerge(I) obs: 0.37 / Rpim(I) all: 0.153 / Rrim(I) all: 0.402 / Net I/σ(I): 3.9 |
Reflection shell | Resolution: 2.5→2.589 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.994 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 2798 / CC1/2: 0.783 / Rpim(I) all: 0.408 / Rrim(I) all: 1.077 / % possible all: 98.52 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 8UP4 8up4 Resolution: 2.5→30.114 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.5 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→30.114 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 14.4543 Å / Origin y: 9.3309 Å / Origin z: 33.7537 Å
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Refinement TLS group | Selection details: all |