+Open data
-Basic information
Entry | Database: PDB / ID: 7v2x | ||||||
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Title | The complex structure of soBcmB and its substrate 1 | ||||||
Components | dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / dioxygenases / complex / bicyclomycin / side way | ||||||
Function / homology | Chem-7QX / 2-OXOGLUTARIC ACID / : Function and homology information | ||||||
Biological species | Streptomyces ossamyceticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0838742992 Å | ||||||
Authors | Wu, L. / Zhou, J.H. | ||||||
Funding support | 1items
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Citation | Journal: Nat Catal / Year: 2023 Title: Enzymatic catalysis favours eight-membered over five-membered ring closure in bicyclomycin biosynthesis Authors: He, J.B. / Wu, L. / Wei, W. / Meng, S. / Liu, Z.T. / Wu, X. / Pan, H.X. / Yang, S. / Liang, Y. / Zhou, J. / Tang, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7v2x.cif.gz | 157.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7v2x.ent.gz | 103.7 KB | Display | PDB format |
PDBx/mmJSON format | 7v2x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7v2x_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7v2x_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7v2x_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | 7v2x_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/7v2x ftp://data.pdbj.org/pub/pdb/validation_reports/v2/7v2x | HTTPS FTP |
-Related structure data
Related structure data | 7v2tSC 7v2uC 7v34C 7v36C 7v3eC 7v3nC 7v3oC 8hivC S: Starting model for refinement 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 , 1 types, 1 molecules A
#1: Protein | Mass: 37291.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces ossamyceticus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) |
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-Non-polymers , 5 types, 101 molecules
#2: Chemical | ChemComp-AKG / |
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#3: Chemical | ChemComp-FE2 / |
#4: Chemical | ChemComp-GOL / |
#5: Chemical | ChemComp-7QX / ( |
#6: 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: 2.58 Å3/Da / Density % sol: 52.3 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES pH 7.0, 2 M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97852 Å / Relative weight: 1 |
Reflection | Resolution: 2.08→47.1302 Å / Num. obs: 23036 / % possible obs: 94.9 % / Redundancy: 31.1 % / Biso Wilson estimate: 38.4256802628 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.104 / Net I/σ(I): 26.7 |
Reflection shell | Resolution: 2.08→2.14 Å / Rmerge(I) obs: 1.633 / Num. unique obs: 1769 / CC1/2: 0.863 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7V2T Resolution: 2.0838742992→47.1301780368 Å / SU ML: 0.223371226136 / Cross valid method: FREE R-VALUE / σ(F): 1.33794794639 / Phase error: 23.9224531452 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: 46.8541370872 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.0838742992→47.1301780368 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 38.7756278357 Å / Origin y: 48.414842226 Å / Origin z: 72.8572824569 Å
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Refinement TLS group | Selection details: all |