+Open data
-Basic information
Entry | Database: PDB / ID: 6k1t | ||||||
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Title | The structure of Francisella virulence factor BioJ | ||||||
Components | Alpha/beta hydrolase fold family protein | ||||||
Keywords | HYDROLASE / virulence factor BioJ | ||||||
Function / homology | Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold / hydrolase activity / Alpha/beta hydrolase fold family protein Function and homology information | ||||||
Biological species | Francisella philomiragia subsp. philomiragia ATCC 25015 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.584 Å | ||||||
Authors | Ouyang, S. / Guan, H. / Zhang, S. | ||||||
Citation | Journal: Iscience / Year: 2019 Title: Molecular Basis of BioJ, a Unique Gatekeeper in Bacterial Biotin Synthesis. Authors: Wei, W. / Guan, H. / Zhu, T. / Zhang, S. / Fan, C. / Ouyang, S. / Feng, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6k1t.cif.gz | 78.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6k1t.ent.gz | 56.6 KB | Display | PDB format |
PDBx/mmJSON format | 6k1t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6k1t_validation.pdf.gz | 426.8 KB | Display | wwPDB validaton report |
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Full document | 6k1t_full_validation.pdf.gz | 429.7 KB | Display | |
Data in XML | 6k1t_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 6k1t_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k1/6k1t ftp://data.pdbj.org/pub/pdb/validation_reports/k1/6k1t | HTTPS FTP |
-Related structure data
Similar structure data |
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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: 35479.434 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Francisella philomiragia subsp. philomiragia ATCC 25015 (bacteria) Gene: BZ13_192 / Production host: Escherichia coli (E. coli) / References: UniProt: C6YW90 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.51 % |
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Crystal grow | Temperature: 289.15 K / Method: counter-diffusion Details: 20% (v/v) PEG 6000, 100mM BICINE/sodium hydroxide (pH 9.0) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 20, 2018 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→51.32 Å / Num. obs: 37190 / % possible obs: 91.5 % / Redundancy: 3 % / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 1.58→1.67 Å / Num. unique obs: 5609 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.584→40.208 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 25.41
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.584→40.208 Å
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Refine LS restraints |
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LS refinement shell |
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