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Yorodumi- PDB-7wux: Crystal structure of AziU3/U2 complexed with (5S,6S)-O7-sulfo DAD... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wux | ||||||||||||
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Title | Crystal structure of AziU3/U2 complexed with (5S,6S)-O7-sulfo DADH from Streptomyces sahachiroi | ||||||||||||
Components |
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Keywords | BIOSYNTHETIC PROTEIN / ES Complex / New Fold / Aziridine synthase / Azinomycin B | ||||||||||||
Function / homology | Butirosin biosynthesis protein H, N-terminal / Butirosin biosynthesis protein H, N-terminal / Chem-6OI / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / TRIETHYLENE GLYCOL / Azi28 / Azi29 Function and homology information | ||||||||||||
Biological species | Streptomyces sahachiroi (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | ||||||||||||
Authors | Kurosawa, S. / Yoshida, A. / Tomita, T. / Nishiyama, M. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2022 Title: Molecular Basis for Enzymatic Aziridine Formation via Sulfate Elimination. Authors: Kurosawa, S. / Hasebe, F. / Okamura, H. / Yoshida, A. / Matsuda, K. / Sone, Y. / Tomita, T. / Shinada, T. / Takikawa, H. / Kuzuyama, T. / Kosono, S. / Nishiyama, M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wux.cif.gz | 427.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wux.ent.gz | 334.7 KB | Display | PDB format |
PDBx/mmJSON format | 7wux.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wux_validation.pdf.gz | 967.4 KB | Display | wwPDB validaton report |
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Full document | 7wux_full_validation.pdf.gz | 976.3 KB | Display | |
Data in XML | 7wux_validation.xml.gz | 47.8 KB | Display | |
Data in CIF | 7wux_validation.cif.gz | 72.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wu/7wux ftp://data.pdbj.org/pub/pdb/validation_reports/wu/7wux | HTTPS FTP |
-Related structure data
Related structure data | 7wuwC 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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Unit cell |
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-Components
-Protein , 2 types, 4 molecules ABCD
#1: Protein | Mass: 25401.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sahachiroi (bacteria) / Plasmid: pET Duet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: B4XYC0 #2: Protein | Mass: 38937.473 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sahachiroi (bacteria) / Plasmid: pET Duet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: B4XYC1 |
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-Non-polymers , 5 types, 1082 molecules
#3: Chemical | ChemComp-PGE / | ||||
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#4: Chemical | ChemComp-P4G / | ||||
#5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-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: 2.22 Å3/Da / Density % sol: 44.47 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% PEG 3350, 0.2M Magnesium formic acid |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 30, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→48.873 Å / Num. obs: 106322 / % possible obs: 99.6 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.032 / Rrim(I) all: 0.06 / Net I/σ(I): 20.4 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.26 / Num. unique obs: 5231 / CC1/2: 0.965 / Rpim(I) all: 0.11 / Rrim(I) all: 0.283 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→48.873 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.121 / SU ML: 0.067 / Cross valid method: FREE R-VALUE / ESU R: 0.115 / ESU R Free: 0.108 Details: Hydrogens have been added in their riding positions
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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: 18.828 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→48.873 Å
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Refine LS restraints |
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LS refinement shell |
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