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Yorodumi- PDB-7cbb: Crystal structure of SbnC in the biosynthesis of staphyloferrin B -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cbb | ||||||
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Title | Crystal structure of SbnC in the biosynthesis of staphyloferrin B | ||||||
Components | IucA/IucC family siderophore biosynthesis protein | ||||||
Keywords | BIOSYNTHETIC PROTEIN / cupped hand fold / Type B NIS synthetase / siderophore synthetase | ||||||
Function / homology | Function and homology information staphyloferrin B synthase / acid-amino acid ligase activity / siderophore biosynthetic process / ATP binding Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å | ||||||
Authors | Tang, J. / Ju, Y. / Zhou, H. | ||||||
Funding support | China, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2020 Title: Structural and Biochemical Characterization of SbnC as a Representative Type B Siderophore Synthetase. Authors: Tang, J. / Ju, Y. / Zhou, J. / Guo, J. / Gu, Q. / Xu, J. / Zhou, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7cbb.cif.gz | 236.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7cbb.ent.gz | 198.7 KB | Display | PDB format |
PDBx/mmJSON format | 7cbb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cb/7cbb ftp://data.pdbj.org/pub/pdb/validation_reports/cb/7cbb | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 68189.641 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: sbnC, DDL17_05250, M1K003_0650 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A389V6N4, UniProt: Q2G1N1*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | 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: 3.98 Å3/Da / Density % sol: 69.09 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M tri-Lithium citrate, 22% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978763716744 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978763716744 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 64879 / % possible obs: 100 % / Redundancy: 13.1 % / Rpim(I) all: 0.029 / Net I/σ(I): 20.7 |
Reflection shell | Resolution: 2.6→2.66 Å / Redundancy: 13.5 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 4487 / Rpim(I) all: 0.209 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.945 / SU B: 8.649 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.325 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.337 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→50 Å
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Refine LS restraints |
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