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Yorodumi- PDB-8k6u: Serial Femtosecond X-ray structure of E.coli Cyanase with un-mode... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8k6u | ||||||
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Title | Serial Femtosecond X-ray structure of E.coli Cyanase with un-modeled density at active site | ||||||
Components | Cyanate hydratase | ||||||
Keywords | LYASE / bi-substrate enzyme / enzyme reaction / room temperature | ||||||
Function / homology | Function and homology information cyanate catabolic process / cyanase / cyanate hydratase activity / DNA binding Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Kim, J. / Nam, K.H. / Cho, Y. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2023 Title: Structural mechanism of Escherichia coli cyanase. Authors: Kim, J. / Kim, Y. / Park, J. / Nam, K.H. / Cho, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8k6u.cif.gz | 311.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8k6u.ent.gz | 252.9 KB | Display | PDB format |
PDBx/mmJSON format | 8k6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8k6u_validation.pdf.gz | 470.7 KB | Display | wwPDB validaton report |
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Full document | 8k6u_full_validation.pdf.gz | 479.8 KB | Display | |
Data in XML | 8k6u_validation.xml.gz | 27.9 KB | Display | |
Data in CIF | 8k6u_validation.cif.gz | 48.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k6/8k6u ftp://data.pdbj.org/pub/pdb/validation_reports/k6/8k6u | HTTPS FTP |
-Related structure data
Related structure data | 8k6gC 8k6hC 8k6sC 8k6xC 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
#1: Protein | Mass: 17481.266 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: cynS, cnt, b0340, JW0331 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P00816, cyanase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.56 Å3/Da / Density % sol: 51.87 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 7.3 Details: 50mM Tris-Cl (pH 7.3), 50 mM potassium phosphate, and 2.5 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: NCI / Wavelength: 1.305 Å |
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: May 22, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.305 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→75.9 Å / Num. obs: 266307 / % possible obs: 100 % / Redundancy: 295.4 % / CC1/2: 0.96 / CC star: 0.99 / R split: 0.18 / Net I/σ(I): 4.54 |
Reflection shell | Resolution: 1.9→2 Å / Mean I/σ(I) obs: 1.41 / Num. unique obs: 18842 / CC1/2: 0.35 / R split: 0.83 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→57.13 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 22.21 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→57.13 Å
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Refine LS restraints |
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LS refinement shell |
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