+Open data
-Basic information
Entry | Database: PDB / ID: 7v57 | ||||||
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Title | Structure of AdaV | ||||||
Components | AdaVGeneral German Workers' Association | ||||||
Keywords | OXIDOREDUCTASE / Halogenase | ||||||
Function / homology | Isopenicillin N synthase-like, Fe(2+) 2OG dioxygenase domain / 2OG-Fe(II) oxygenase superfamily / Isopenicillin N synthase-like superfamily / 2-OXOGLUTARIC ACID / : / Isopenicillin N synthase-like Fe(2+) 2OG dioxygenase domain-containing protein Function and homology information | ||||||
Biological species | Actinomadura sp. ATCC 39365 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å | ||||||
Authors | Zhang, Z.Y. / Chen, W.Q. / Zhai, G.Q. / Zhang, M. | ||||||
Funding support | China, 1items
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Citation | Journal: Acs Catalysis / Year: 2022 Title: Structural Insight into the Catalytic Mechanism of Non-Heme Iron Halogenase AdaV in 2'-Chloropentostatin Biosynthesis Authors: Zhai, G.Q. / Gong, R. / Lin, Y. / Zhang, M. / Li, J. / Deng, Z. / Sun, J. / Chen, W. / Zhang, Z.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7v57.cif.gz | 64.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7v57.ent.gz | 47.2 KB | Display | PDB format |
PDBx/mmJSON format | 7v57.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/7v57 ftp://data.pdbj.org/pub/pdb/validation_reports/v5/7v57 | HTTPS FTP |
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-Related structure data
Related structure data | 7fh5C 7v52C 7v54C 7v56C 7v7xC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 35947.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Actinomadura sp. ATCC 39365 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1U8X168 |
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#2: Chemical | ChemComp-FE / |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-AKG / |
#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: 3.76 Å3/Da / Density % sol: 67.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.085 M HEPES sodium pH 7.5, 1.7% v/v Polyethylene glycol 400, 1.7 M Ammonium sulfate, 15% v/v Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 20, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→19.85 Å / Num. obs: 22606 / % possible obs: 99.8 % / Redundancy: 20 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 2.35→2.44 Å / Rmerge(I) obs: 0.947 / Num. unique obs: 2359 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.35→19.85 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.61 / Stereochemistry target values: ML
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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: 114.55 Å2 / Biso mean: 51.7592 Å2 / Biso min: 30.27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.35→19.85 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8 / % reflection obs: 100 %
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