+Open data
-Basic information
Entry | Database: PDB / ID: 8a90 | ||||||
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Title | Crystal structure of FrsH | ||||||
Components | Non-heme diiron monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / NRPS | ||||||
Function / homology | Diiron non-heme beta-hydroxylase, N-terminal domain / Diiron non-heme beta-hydroxylase N-terminal domain / Beta-lactamase superfamily domain / monooxygenase activity / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / ACETATE ION / : / OXYGEN ATOM / Non-heme diiron monooxygenase Function and homology information | ||||||
Biological species | Chromobacterium vaccinii (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.574 Å | ||||||
Authors | Schneberger, N. / Wirtz, D.A. / Cruesemann, M. / Hagelueken, G. | ||||||
Funding support | 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2023 Title: Adenylation Domain-Guided Recruitment of Trans- Acting Nonheme Monooxygenases in Nonribosomal Peptide Biosynthesis. Authors: Wirtz, D.A. / Schneberger, N. / Kloppel, S. / Richarz, R. / Geyer, M. / Konig, G.M. / Hagelueken, G. / Crusemann, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a90.cif.gz | 271.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a90.ent.gz | 177.2 KB | Display | PDB format |
PDBx/mmJSON format | 8a90.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8a90_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 8a90_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 8a90_validation.xml.gz | 23.8 KB | Display | |
Data in CIF | 8a90_validation.cif.gz | 35.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a9/8a90 ftp://data.pdbj.org/pub/pdb/validation_reports/a9/8a90 | HTTPS FTP |
-Related structure data
Related structure data | 4jo0S S: Starting model for refinement |
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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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 4 - 531 / Label seq-ID: 4 - 531
NCS oper: (Code: givenMatrix: (-0.346109814363, -0.82662189853, 0.443738924676), (-0.835612433918, 0.0565613263848, -0.546399740702), (0.426567528867, -0.559908075695, -0.710311966735)Vector: 74. ...NCS oper: (Code: given Matrix: (-0.346109814363, -0.82662189853, 0.443738924676), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 60273.219 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chromobacterium vaccinii (bacteria) / Gene: frsH / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7S9SWM2 |
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-Non-polymers , 5 types, 66 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-FE / #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: 3.37 Å3/Da / Density % sol: 63.46 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion, sitting drop Details: 0.10 M HEPES pH 7.8, 10.89% (w/v) PEG 20000, 0.08 M KAc, 1.36% glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999987 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999987 Å / Relative weight: 1 |
Reflection | Resolution: 2.574→48.02 Å / Num. obs: 87244 / % possible obs: 93.03 % / Redundancy: 4.2 % / Biso Wilson estimate: 54.27 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.151 / Net I/σ(I): 7.22 |
Reflection shell | Resolution: 2.574→2.665 Å / Mean I/σ(I) obs: 1.01 / Num. unique obs: 4482 / CC1/2: 0.458 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4jo0 Resolution: 2.574→48.02 Å / SU ML: 0.4679 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.2121 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 58.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.574→48.02 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.878145075047 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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