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Yorodumi- PDB-5yog: Crystal Structure of flavodoxin with engineered disulfide bond N1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yog | ||||||
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Title | Crystal Structure of flavodoxin with engineered disulfide bond N14C-C93 | ||||||
Components | Flavodoxin | ||||||
Keywords | ELECTRON TRANSPORT / fusion partner / FMN-binding protein / oxidation | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Desulfovibrio vulgaris (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å | ||||||
Authors | Pu, M. / Xu, Z. / Song, G. / Liu, Z.J. | ||||||
Citation | Journal: Protein Cell / Year: 2018 Title: Protein crystal quality oriented disulfide bond engineering. Authors: Pu, M. / Xu, Z. / Peng, Y. / Hou, Y. / Liu, D. / Wang, Y. / Liu, H. / Song, G. / Liu, Z.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5yog.cif.gz | 50.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yog.ent.gz | 33.9 KB | Display | PDB format |
PDBx/mmJSON format | 5yog.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yog_validation.pdf.gz | 783.3 KB | Display | wwPDB validaton report |
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Full document | 5yog_full_validation.pdf.gz | 784.5 KB | Display | |
Data in XML | 5yog_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 5yog_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/5yog ftp://data.pdbj.org/pub/pdb/validation_reports/yo/5yog | HTTPS FTP |
-Related structure data
Related structure data | 5ym7C 5yo3C 5yo4C 5yo5C 5yo6C 5yobC 5yocC 5yoeC 1j8qS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15761.262 Da / Num. of mol.: 1 / Mutation: N14C, Y98W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303) (bacteria) Strain: Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303 / Gene: DVU_2680 / Production host: Escherichia coli (E. coli) / References: UniProt: P00323 | ||||
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#2: Chemical | ChemComp-FMN / | ||||
#3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: 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: 2.36 Å3/Da / Density % sol: 47.96 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: Tris-HCL buffer, pH 7.3 Ammonium Sulfate 3.1M |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Jul 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.42→32.917 Å / Num. obs: 27376 / % possible obs: 99 % / Redundancy: 5.5 % / Net I/σ(I): 21.67 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1J8Q Resolution: 1.42→32.917 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 16.99
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.42→32.917 Å
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Refine LS restraints |
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LS refinement shell |
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