+Open data
-Basic information
Entry | Database: PDB / ID: 8hiv | ||||||
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Title | The structure of apo-SoBcmB with Fe(II) and AKG | ||||||
Components | Fe/2OG dependent dioxygenase | ||||||
Keywords | OXIDOREDUCTASE / apo-form / bicyclomycin / dioxygenase | ||||||
Function / homology | 2-OXOGLUTARIC ACID / : Function and homology information | ||||||
Biological species | Streptomyces ossamyceticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2000308002 Å | ||||||
Authors | Wu, L. / Zhou, J.H. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: The structure of apo-SoBcmB with Fe(II) and AKG 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 | 8hiv.cif.gz | 80.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8hiv.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 8hiv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/8hiv ftp://data.pdbj.org/pub/pdb/validation_reports/hi/8hiv | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#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 (E. coli) |
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#2: Chemical | ChemComp-AKG / |
#3: Chemical | ChemComp-FE2 / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.17 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 1M Potassium chloride, 0.1M HEPES pH 7, 1M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→44.03 Å / Num. obs: 20954 / % possible obs: 100 % / Redundancy: 12 % / Biso Wilson estimate: 25.061 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.032 / Rrim(I) all: 0.115 / Net I/σ(I): 17.2 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.942 / Mean I/σ(I) obs: 5.1 / Num. unique obs: 1769 / CC1/2: 0.873 / Rpim(I) all: 0.264 / Rrim(I) all: 0.979 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2000308002→26.7825539092 Å / SU ML: 0.239438880972 / Cross valid method: FREE R-VALUE / σ(F): 1.33484361805 / Phase error: 21.7743709606 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: 39.0559365877 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2000308002→26.7825539092 Å
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Refine LS restraints |
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LS refinement shell |
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