+Open data
-Basic information
Entry | Database: PDB / ID: 7v2u | ||||||
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Title | The complex structure of SoBcmB and its product 2f | ||||||
Components | dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / complex / bicyclomycin / dioxygenases | ||||||
Function / homology | Chem-8KI / 2-OXOGLUTARIC ACID / : Function and homology information | ||||||
Biological species | Streptomyces ossamyceticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.00009920726 Å | ||||||
Authors | Wu, L. / Zhou, J.H. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: The complex structure of SoBcmB and its product 2f Authors: Wu, L. / Zhou, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7v2u.cif.gz | 90.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7v2u.ent.gz | 54.7 KB | Display | PDB format |
PDBx/mmJSON format | 7v2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7v2u_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7v2u_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7v2u_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 7v2u_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v2/7v2u ftp://data.pdbj.org/pub/pdb/validation_reports/v2/7v2u | HTTPS FTP |
-Related structure data
Related structure data | 7v2tS 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 on special symmetry positions |
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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 , 6 types, 151 molecules
#2: Chemical | ChemComp-AKG / | ||||
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#3: Chemical | ChemComp-FE2 / | ||||
#4: Chemical | ChemComp-8KI / ( | ||||
#5: Chemical | #6: Chemical | ChemComp-CL / | #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: 2.62 Å3/Da / Density % sol: 52.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M HEPES pH 7.0, 1 M Ammonium sulfate, 1 M potassium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1.03315 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03315 Å / Relative weight: 1 |
Reflection | Resolution: 2→19.8814 Å / Num. obs: 27599 / % possible obs: 99.9 % / Redundancy: 37.8 % / Biso Wilson estimate: 28.0304270345 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.124 / Net I/σ(I): 29 |
Reflection shell | Resolution: 2→2.05 Å / Rmerge(I) obs: 1.234 / Num. unique obs: 1988 / CC1/2: 0.936 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7V2T Resolution: 2.00009920726→19.8813893511 Å / SU ML: 0.246244257304 / Cross valid method: FREE R-VALUE / σ(F): 1.33426252639 / Phase error: 23.5245866373 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: 29.1766400392 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.00009920726→19.8813893511 Å
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Refine LS restraints |
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LS refinement shell |
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