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Yorodumi- PDB-5yo3: Crystal Structure of B562RIL with engineered disulfide bond V16C-A29C -
+Open data
-Basic information
Entry | Database: PDB / ID: 5yo3 | ||||||
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Title | Crystal Structure of B562RIL with engineered disulfide bond V16C-A29C | ||||||
Components | Soluble cytochrome b562 | ||||||
Keywords | ELECTRON TRANSPORT / hemoprotein / fusion partner / helix bundle | ||||||
Function / homology | Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / electron transport chain / periplasmic space / electron transfer activity / iron ion binding / heme binding / Soluble cytochrome b562 Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 | 5yo3.cif.gz | 61.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5yo3.ent.gz | 43.7 KB | Display | PDB format |
PDBx/mmJSON format | 5yo3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5yo3_validation.pdf.gz | 428.3 KB | Display | wwPDB validaton report |
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Full document | 5yo3_full_validation.pdf.gz | 428.9 KB | Display | |
Data in XML | 5yo3_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 5yo3_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/5yo3 ftp://data.pdbj.org/pub/pdb/validation_reports/yo/5yo3 | HTTPS FTP |
-Related structure data
Related structure data | 5ym7C 5yo4C 5yo5C 5yo6C 5yobC 5yocC 5yoeC 5yogC 1m6tS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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 on special symmetry positions |
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-Components
#1: Protein | Mass: 11908.384 Da / Num. of mol.: 1 / Mutation: M7W, V16C, A29C, H102I, R106L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cybC / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABE7 | ||
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#2: Chemical | ChemComp-SO4 / #3: 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 Å3/Da / Density % sol: 38.4 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: NH4(SO4), Bicine, N-octanoylsucrose / PH range: 9.0-9.4 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: Liquid nitrogen |
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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 15, 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: 1.7→47.118 Å / Num. obs: 10312 / % possible obs: 95 % / Redundancy: 4.4 % / Biso Wilson estimate: 16.76 Å2 / Net I/σ(I): 55.71 |
Reflection shell | Resolution: 1.7→1.78 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1M6T Resolution: 1.7→47.118 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.94 / 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: 1.7→47.118 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 16.4812 Å / Origin y: 3.0592 Å / Origin z: -11.2233 Å
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Refinement TLS group | Selection details: chain 'A' and resid 0 through 106 |