+Open data
-Basic information
Entry | Database: PDB / ID: 8u1i | ||||||
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Title | Crystal structure of SyoA bound to 4-methylsyringol | ||||||
Components | Cytochrome P450 | ||||||
Keywords | OXIDOREDUCTASE / Cytochrome P450 / O-demethylase / peroxygenase | ||||||
Function / homology | PROTOPORPHYRIN IX CONTAINING FE / NITRATE ION / : Function and homology information | ||||||
Biological species | Amycolatopsis thermoflava N1165 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å | ||||||
Authors | Harlington, A.C. / Shearwin, K.E. / Bell, S.G. / Whelan, F. | ||||||
Funding support | Australia, 1items
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Citation | Journal: To Be Published Title: Structural insights into the S-lignin O-demethylase SyoA Authors: Harlington, A.C. / Shearwin, K.E. / Bell, S.G. / Whelan, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8u1i.cif.gz | 235.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8u1i.ent.gz | 155 KB | Display | PDB format |
PDBx/mmJSON format | 8u1i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8u1i_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8u1i_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 8u1i_validation.xml.gz | 20.4 KB | Display | |
Data in CIF | 8u1i_validation.cif.gz | 32 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u1/8u1i ftp://data.pdbj.org/pub/pdb/validation_reports/u1/8u1i | HTTPS FTP |
-Related structure data
Related structure data | 8u09C 8u19SC C: citing same article (ref.) 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
#1: Protein | Mass: 45625.430 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Amycolatopsis thermoflava N1165 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) / References: unspecific monooxygenase | ||||
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#2: Chemical | ChemComp-HEM / | ||||
#3: Chemical | ChemComp-UB9 / Mass: 168.190 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12O3 / Feature type: SUBJECT OF INVESTIGATION | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.72 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: 0.2 M lithium nitrate, 20% w/v PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 17, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→41.6 Å / Num. obs: 153831 / % possible obs: 99.95 % / Redundancy: 6.7 % / Biso Wilson estimate: 11.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.0695 / Net I/σ(I): 11.41 |
Reflection shell | Resolution: 1.12→1.16 Å / Rmerge(I) obs: 1.213 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 92855 / CC1/2: 0.626 / % possible all: 99.93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 8U19 Resolution: 1.12→41.6 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.1885 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.12→41.6 Å
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Refine LS restraints |
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LS refinement shell |
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