+Open data
-Basic information
Entry | Database: PDB / ID: 6qep | ||||||
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Title | EngBF DARPin Fusion 4b H14 | ||||||
Components | PEGA domain-containing protein,EngBF-DARPin Fusion 4b H14 | ||||||
Keywords | HYDROLASE / crystallization chaperone / protein fusion / DARPin / chaperone | ||||||
Function / homology | : / : Function and homology information | ||||||
Biological species | Bifidobacterium longum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 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 | 6qep.cif.gz | 549.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qep.ent.gz | 446.7 KB | Display | PDB format |
PDBx/mmJSON format | 6qep.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qep_validation.pdf.gz | 452.2 KB | Display | wwPDB validaton report |
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Full document | 6qep_full_validation.pdf.gz | 469.7 KB | Display | |
Data in XML | 6qep_validation.xml.gz | 51.1 KB | Display | |
Data in CIF | 6qep_validation.cif.gz | 75.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/6qep ftp://data.pdbj.org/pub/pdb/validation_reports/qe/6qep | HTTPS FTP |
-Related structure data
Related structure data | 6qevC 6qfkC 6qfoC 6sh9C C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.18430/m36qep / 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: 147617.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bifidobacterium longum (bacteria) / Gene: DXD52_03130 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A374RF80 | ||
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#2: Chemical | ChemComp-MPD / ( | ||
#3: Chemical | ChemComp-MES / | ||
#4: Chemical | ChemComp-MN / #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: 4.5 Å3/Da / Density % sol: 72.66 % |
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Crystal grow | Temperature: 277.15 K / Method: vapor diffusion / pH: 6.1 Details: MPD, PEG 20,000, sodium chloride, manganese chloride, MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99987 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99987 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→46.28 Å / Num. obs: 80365 / % possible obs: 99.91 % / Redundancy: 20.9 % / Biso Wilson estimate: 81.65 Å2 / Rrim(I) all: 0.172 / Net I/σ(I): 16.78 |
Reflection shell | Resolution: 2.6→2.693 Å / Rrim(I) all: 3.263 |
-Processing
Software |
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Refinement | Resolution: 2.6→46.28 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.249 / SU Rfree Blow DPI: 0.203 / SU Rfree Cruickshank DPI: 0.206
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Displacement parameters | Biso mean: 89.26 Å2
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Refine analyze | Luzzati coordinate error obs: 0.31 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.6→46.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.62 Å / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Origin x: 78.3044 Å / Origin y: -29.716 Å / Origin z: 0.0517 Å
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Refinement TLS group | Selection details: { A|* } |