+Open data
-Basic information
Entry | Database: PDB / ID: 7fe0 | ||||||||||||||||||||||||
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Title | AvmM Catalyzes Macrocyclization in Alchivemycin A Biosynthesis | ||||||||||||||||||||||||
Components | AvmM | ||||||||||||||||||||||||
Keywords | BIOSYNTHETIC PROTEIN / Alchivemycin / Michael addition / Macrocyclization | ||||||||||||||||||||||||
Function / homology | CACODYLATE ION Function and homology information | ||||||||||||||||||||||||
Biological species | Streptomyces sp. NBRC 109436 (bacteria) | ||||||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||||||||||||||||||||
Authors | Zhang, B. / Ge, H.M. | ||||||||||||||||||||||||
Funding support | China, 7items
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Citation | Journal: Nat Commun / Year: 2022 Title: AvmM catalyses macrocyclization through dehydration/Michael-type addition in alchivemycin A biosynthesis. Authors: Zhu, H.J. / Zhang, B. / Wei, W. / Liu, S.H. / Xiang, L. / Zhu, J. / Jiao, R.H. / Igarashi, Y. / Bashiri, G. / Liang, Y. / Tan, R.X. / Ge, H.M. | ||||||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fe0.cif.gz | 240.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fe0.ent.gz | 197.2 KB | Display | PDB format |
PDBx/mmJSON format | 7fe0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7fe0_validation.pdf.gz | 455.1 KB | Display | wwPDB validaton report |
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Full document | 7fe0_full_validation.pdf.gz | 458.9 KB | Display | |
Data in XML | 7fe0_validation.xml.gz | 23.4 KB | Display | |
Data in CIF | 7fe0_validation.cif.gz | 32.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fe/7fe0 ftp://data.pdbj.org/pub/pdb/validation_reports/fe/7fe0 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 24142.221 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. NBRC 109436 (bacteria) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) #2: Chemical | #3: Chemical | ChemComp-CAC / | #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.3 Å3/Da / Density % sol: 46.6 % |
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Crystal grow | Temperature: 295.15 K / Method: vapor diffusion, sitting drop Details: 0.2 M Magnesium acetate tetrahydrate, 0.1 M Sodium cacodylate 6.5 and 20 % w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97919 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 30, 2020 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97919 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.2→23.56 Å / Num. obs: 34785 / % possible obs: 98.3 % / Redundancy: 11.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.144 / Rpim(I) all: 0.041 / Rrim(I) all: 0.15 / Net I/σ(I): 10.3 / Num. measured all: 406516 / Scaling rejects: 4404 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→23.14 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.67 / Stereochemistry target values: MLHL
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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 max: 171.91 Å2 / Biso mean: 49.7072 Å2 / Biso min: 28.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→23.14 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12
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Refinement TLS params. | Method: refined / Origin x: 30.7599 Å / Origin y: 1.6424 Å / Origin z: 102.9689 Å
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Refinement TLS group |
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