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Yorodumi- PDB-7a4t: Crystal structure of the GCN coiled-coil in complex with nanobody Nb39 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7a4t | ||||||||||||
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Title | Crystal structure of the GCN coiled-coil in complex with nanobody Nb39 | ||||||||||||
Components |
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Keywords | DE NOVO PROTEIN / coiled-coil / nanobody / antibody / protein design | ||||||||||||
Function / homology | ACETYL GROUP / : Function and homology information | ||||||||||||
Biological species | Lama glama (llama) Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.124 Å | ||||||||||||
Authors | Hadzi, S. | ||||||||||||
Funding support | European Union, Slovenia, 3items
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Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2021 Title: A nanobody toolbox targeting dimeric coiled-coil modules for functionalization of designed protein origami structures. Authors: Majerle, A. / Hadzi, S. / Aupic, J. / Satler, T. / Lapenta, F. / Strmsek, Z. / Lah, J. / Loris, R. / Jerala, R. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7a4t.cif.gz | 87.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a4t.ent.gz | 65.7 KB | Display | PDB format |
PDBx/mmJSON format | 7a4t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7a4t_validation.pdf.gz | 345.4 KB | Display | wwPDB validaton report |
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Full document | 7a4t_full_validation.pdf.gz | 345.7 KB | Display | |
Data in XML | 7a4t_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 7a4t_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/7a4t ftp://data.pdbj.org/pub/pdb/validation_reports/a4/7a4t | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Antibody / Protein/peptide , 2 types, 3 molecules ABC
#1: Antibody | Mass: 14783.189 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
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#2: Protein/peptide | Mass: 3383.868 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PZY2 |
-Non-polymers , 4 types, 103 molecules
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-ACE / | #5: Chemical | ChemComp-EDO / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 2.34 Å3/Da / Density % sol: 47.54 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium formate 20 % w/v PEG 3350 / PH range: 7.2-8.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980127 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 10, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.980127 Å / Relative weight: 1 |
Reflection | Resolution: 2.124→47.691 Å / Num. obs: 12227 / % possible obs: 99.93 % / Redundancy: 20 % / Biso Wilson estimate: 41.61 Å2 / CC1/2: 1 / Rrim(I) all: 0.121 / Net I/σ(I): 27.45 |
Reflection shell | Resolution: 2.125→2.201 Å / Num. unique obs: 1177 / CC1/2: 0.859 / % possible all: 99.75 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Modeler Resolution: 2.124→47.691 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.02 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 142.54 Å2 / Biso mean: 53.3997 Å2 / Biso min: 24.37 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.124→47.691 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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