+Open data
-Basic information
Entry | Database: PDB / ID: 6xzf | |||||||||
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Title | Nanobody in complex with eGFP | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / Nanobody | |||||||||
Function / homology | Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / TERBIUM(III) ION / Green fluorescent protein Function and homology information | |||||||||
Biological species | Lama glama (llama) Aequorea victoria (jellyfish) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å | |||||||||
Authors | Pompidor, G. / Zimmermann, S. / Loew, C. / Schneider, T. | |||||||||
Citation | Journal: To Be Published Title: Engineered nanobodies with a lanthanide binding motif for crystallographic phasing Authors: Pompidor, G. / Zimmermann, S. / Loew, C. / Schneider, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xzf.cif.gz | 154.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xzf.ent.gz | 118.2 KB | Display | PDB format |
PDBx/mmJSON format | 6xzf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xzf_validation.pdf.gz | 436 KB | Display | wwPDB validaton report |
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Full document | 6xzf_full_validation.pdf.gz | 437.5 KB | Display | |
Data in XML | 6xzf_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 6xzf_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xz/6xzf ftp://data.pdbj.org/pub/pdb/validation_reports/xz/6xzf | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26825.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aequorea victoria (jellyfish) / References: UniProt: P42212*PLUS |
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#2: Antibody | Mass: 14862.208 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) |
#3: Chemical | ChemComp-TB / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.1 M NaAcetate pH 4.6 8 % PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.0332 Å | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 1.69→48.95 Å / Num. obs: 52868 / % possible obs: 98.3 % / Redundancy: 18.7 % / CC1/2: 1 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.016 / Rrim(I) all: 0.068 / Net I/σ(I): 22.4 / Num. measured all: 989184 / Scaling rejects: 10 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.8→48.95 Å / SU ML: 0.1687 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.5369 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 40.19 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→48.95 Å
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Refine LS restraints |
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LS refinement shell |
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