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Yorodumi- PDB-6oyc: Glycosylation Associate Protein (Gap123) complex from Streptococc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6oyc | ||||||
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Title | Glycosylation Associate Protein (Gap123) complex from Streptococcus agalactiae | ||||||
Components | (Glycosylation Associate Protein ...) x 3 | ||||||
Keywords | SUGAR BINDING PROTEIN / Glycosylation / Secretion / lectin | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus agalactiae serotype V | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.351 Å | ||||||
Authors | zhang, H. / Wu, H. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Glycosylation Associate Protein (Gap123) complex from Streptococcus agalactiae Authors: zhang, H. / Zhu, F. / Wu, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6oyc.cif.gz | 289.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oyc.ent.gz | 230.4 KB | Display | PDB format |
PDBx/mmJSON format | 6oyc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6oyc_validation.pdf.gz | 280.5 KB | Display | wwPDB validaton report |
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Full document | 6oyc_full_validation.pdf.gz | 281.8 KB | Display | |
Data in XML | 6oyc_validation.xml.gz | 2 KB | Display | |
Data in CIF | 6oyc_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oy/6oyc ftp://data.pdbj.org/pub/pdb/validation_reports/oy/6oyc | HTTPS FTP |
-Related structure data
Related structure data | 6e2i S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Glycosylation Associate Protein ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 60541.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R) (bacteria) Strain: ATCC BAA-611 / 2603 V/R / Gene: SAG1452 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8DYM4 |
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#2: Protein | Mass: 59251.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R) (bacteria) Strain: ATCC BAA-611 / 2603 V/R / Gene: SAG1451 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8DYM5 |
#3: Protein | Mass: 37928.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae serotype V (strain ATCC BAA-611 / 2603 V/R) (bacteria) Strain: ATCC BAA-611 / 2603 V/R / Gene: SAG1450 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8DYM6 |
-Non-polymers , 3 types, 419 molecules
#4: Chemical | ChemComp-GOL / #5: Chemical | #6: Water | ChemComp-HOH / | |
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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: 2.83 Å3/Da / Density % sol: 56.54 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES pH 7.5, 5% PEG 400, 2M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 15, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→49.272 Å / Num. obs: 72701 / % possible obs: 99.55 % / Redundancy: 14.1 % / Net I/σ(I): 28.13 |
Reflection shell | Resolution: 2.35→2.43 Å / Num. unique obs: 7084 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6E2I 6e2i Resolution: 2.351→49.272 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.21
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.351→49.272 Å
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Refine LS restraints |
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LS refinement shell |
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