+Open data
-Basic information
Entry | Database: PDB / ID: 6qev | ||||||
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Title | EngBF DARPin Fusion 4b B6 | ||||||
Components |
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Keywords | HYDROLASE / crystallization chaperone / protein fusion / DARPin / CHAPERONE | ||||||
Function / homology | Function and homology information endo-alpha-N-acetylgalactosaminidase activity / carbohydrate binding / membrane => GO:0016020 Similarity search - Function | ||||||
Biological species | Bifidobacterium longum (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å | ||||||
Authors | Ernst, P. / Pluckthun, A. / Mittl, P.R.E. | ||||||
Citation | Journal: Sci Rep / Year: 2019 Title: Structural analysis of biological targets by host:guest crystal lattice engineering. Authors: Ernst, P. / Pluckthun, A. / Mittl, P.R.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qev.cif.gz | 535.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qev.ent.gz | 447.9 KB | Display | PDB format |
PDBx/mmJSON format | 6qev.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qev_validation.pdf.gz | 456 KB | Display | wwPDB validaton report |
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Full document | 6qev_full_validation.pdf.gz | 466.2 KB | Display | |
Data in XML | 6qev_validation.xml.gz | 50.9 KB | Display | |
Data in CIF | 6qev_validation.cif.gz | 74.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/6qev ftp://data.pdbj.org/pub/pdb/validation_reports/qe/6qev | HTTPS FTP |
-Related structure data
Related structure data | 6qepC 6qfkC 6qfoC 6sh9C C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.18430/m36qev / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 147845.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium longum (bacteria) / Gene: DW792_04840 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A414FD23 | ||||
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#2: Protein/peptide | Mass: 1603.862 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) | ||||
#3: Chemical | ChemComp-MN / #4: Chemical | #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: 4.53 Å3/Da / Density % sol: 72.86 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion / pH: 6 Details: MPD, sodium chloride, manganese chloride, PEG 20,000, MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.999 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.999 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→48.69 Å / Num. obs: 73165 / % possible obs: 99.82 % / Redundancy: 17.6 % / Biso Wilson estimate: 91.69 Å2 / Rrim(I) all: 0.3377 / Net I/σ(I): 8.59 |
Reflection shell | Resolution: 2.7→2.797 Å / Rrim(I) all: 3.03 |
-Processing
Software |
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Refinement | Resolution: 2.7→48.69 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.286 / SU Rfree Blow DPI: 0.224 / SU Rfree Cruickshank DPI: 0.228
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Displacement parameters | Biso mean: 71.92 Å2
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Refine analyze | Luzzati coordinate error obs: 0.33 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.7→48.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.72 Å / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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