+Open data
-Basic information
Entry | Database: PDB / ID: 8aq8 | ||||||||||||||||||
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Title | FAD-dependent monooxygenase from Stenotrophomonas maltophilia | ||||||||||||||||||
Components | Monooxygenase | ||||||||||||||||||
Keywords | OXIDOREDUCTASE / Monooxygenase / FAD-dependent / Antibiotic resistance | ||||||||||||||||||
Function / homology | FAD-binding domain / FAD binding domain / monooxygenase activity / FAD binding / FAD/NAD(P)-binding domain superfamily / FLAVIN-ADENINE DINUCLEOTIDE / NITRATE ION / DI(HYDROXYETHYL)ETHER / Monooxygenase Function and homology information | ||||||||||||||||||
Biological species | Stenotrophomonas maltophilia (bacteria) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||||||||||||||
Authors | Maly, M. / Kolenko, P. / Duskova, J. / Skalova, T. / Dohnalek, J. | ||||||||||||||||||
Funding support | European Union, Czech Republic, 5items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2023 Title: Tetracycline-modifying enzyme SmTetX from Stenotrophomonas maltophilia. Authors: Maly, M. / Kolenko, P. / Stransky, J. / Svecova, L. / Duskova, J. / Koval', T. / Skalova, T. / Trundova, M. / Adamkova, K. / Cerny, J. / Bozikova, P. / Dohnalek, J. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8aq8.cif.gz | 316.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8aq8.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8aq8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8aq8_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8aq8_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 8aq8_validation.xml.gz | 60.8 KB | Display | |
Data in CIF | 8aq8_validation.cif.gz | 90.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/8aq8 ftp://data.pdbj.org/pub/pdb/validation_reports/aq/8aq8 | HTTPS FTP |
-Related structure data
Related structure data | 6n04S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/956 / Data set type: diffraction image data / Metadata reference: 10.15785/SBGRID/956 |
Other databases |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: THR / End label comp-ID: THR / Auth seq-ID: 3 - 357 / Label seq-ID: 5 - 359
NCS ensembles :
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-Components
-Protein , 1 types, 4 molecules AAABBBCCCDDD
#1: Protein | Mass: 39179.293 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: FAD-dependent protein. The reference UniProt sequence A0A2Y9UCL1 is not the sequence of the target protein. The real sequence of the target protein is the NCBI reference sequence WP_ ...Details: FAD-dependent protein. The reference UniProt sequence A0A2Y9UCL1 is not the sequence of the target protein. The real sequence of the target protein is the NCBI reference sequence WP_049406473.1 from the complete genome of Stenotrophomonas maltophilia, strain AB550, GenBank entry CP028899.1. Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria) Gene: B9Y88_09170 / Plasmid: pET28a+TEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Lemo / References: UniProt: A0A2Y9UCL1 |
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-Non-polymers , 7 types, 1132 molecules
#2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-EDO / #4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-CL / #8: 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: 2.6 Å3/Da / Density % sol: 53 % / Description: Plate-shaped |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12% (w/v) PEG 8000, 24% (v/v) ethylene glycol, 60 mM sodium nitrate, 60 mM disodium hydrogen phosphate, 60 mM ammonium sulfate, 100 mM MES/imidazole pH 6.5, 4% acetone |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→48.26 Å / Num. obs: 98291 / % possible obs: 85.3 % / Observed criterion σ(I): -3.7 / Redundancy: 4.8 % / Biso Wilson estimate: 39 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.07 / Rrim(I) all: 0.156 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 1.95→2.01 Å / Redundancy: 5.2 % / Rmerge(I) obs: 1.531 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4915 / CC1/2: 0.378 / Rpim(I) all: 0.729 / Rrim(I) all: 1.702 / % possible all: 48.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6N04 Resolution: 1.95→48.26 Å / Cor.coef. Fo:Fc: 0.95 / SU B: 5.09 / SU ML: 0.131 / Cross valid method: FREE R-VALUE / ESU R: 0.201
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.9 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→48.26 Å
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Refine LS restraints |
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