+Open data
-Basic information
Entry | Database: PDB / ID: 6qfk | ||||||
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Title | EngBF DARPin Fusion 4b G10 | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2 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 | 6qfk.cif.gz | 572.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qfk.ent.gz | 458 KB | Display | PDB format |
PDBx/mmJSON format | 6qfk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qfk_validation.pdf.gz | 479.5 KB | Display | wwPDB validaton report |
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Full document | 6qfk_full_validation.pdf.gz | 488.9 KB | Display | |
Data in XML | 6qfk_validation.xml.gz | 63.1 KB | Display | |
Data in CIF | 6qfk_validation.cif.gz | 98.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/6qfk ftp://data.pdbj.org/pub/pdb/validation_reports/qf/6qfk | HTTPS FTP |
-Related structure data
Related structure data | 6qepC 6qevC 6qfoC 6sh9C 2zxqS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.18430/m36qfk / 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
-Protein / Protein/peptide , 2 types, 2 molecules AB
#1: Protein | Mass: 148007.688 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) |
-Non-polymers , 5 types, 1656 molecules
#3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-MPD / ( | #5: Chemical | ChemComp-EDO / #6: Chemical | #7: 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 grow | Temperature: 277.15 K / Method: vapor diffusion / pH: 6.6 Details: MPD, PEG 20,000, MES, sodium chloride, manganese chloride |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→46.33 Å / Num. obs: 174930 / % possible obs: 99.98 % / Redundancy: 20.9 % / Biso Wilson estimate: 39.31 Å2 / Rrim(I) all: 0.2538 / Net I/σ(I): 13.46 |
Reflection shell | Resolution: 2→2.072 Å / Rrim(I) all: 2.903 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2ZXQ Resolution: 2→29.25 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU R Cruickshank DPI: 0.096 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.102 / SU Rfree Blow DPI: 0.097 / SU Rfree Cruickshank DPI: 0.093
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Displacement parameters | Biso mean: 46.46 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2→29.25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.01 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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