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Yorodumi- PDB-6ir1: Crystal structure of red fluorescent protein mCherry complexed wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ir1 | |||||||||
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Title | Crystal structure of red fluorescent protein mCherry complexed with the nanobody LaM4 at 1.9 Angstron resolution | |||||||||
Components |
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Keywords | FLUORESCENT PROTEIN / Complex / Nanobody / red fluorescent protein mCherry / LaM4 | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Anaplasma marginale (bacteria) Camelus bactrianus (Bactrian camel) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.919 Å | |||||||||
Authors | Ding, Y. / Wang, Z.Y. / Hu, R.T. / Chen, X. | |||||||||
Funding support | China, 2items
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Citation | Journal: Protein Sci. / Year: 2021 Title: Structural insights into the binding of nanobodies LaM2 and LaM4 to the red fluorescent protein mCherry. Authors: Wang, Z. / Li, L. / Hu, R. / Zhong, P. / Zhang, Y. / Cheng, S. / Jiang, H. / Liu, R. / Ding, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ir1.cif.gz | 142.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ir1.ent.gz | 110.3 KB | Display | PDB format |
PDBx/mmJSON format | 6ir1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ir/6ir1 ftp://data.pdbj.org/pub/pdb/validation_reports/ir/6ir1 | HTTPS FTP |
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-Related structure data
Related structure data | 6ir2C 2h5qS 3k1kS S: Starting model for refinement C: citing same article (ref.) |
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Similar 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
#1: Protein | Mass: 26797.229 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anaplasma marginale (bacteria) / Gene: mCherry / Production host: Escherichia coli (E. coli) / References: UniProt: X5DSL3 |
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#2: Antibody | Mass: 14021.442 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelus bactrianus (Bactrian camel) / Production host: Escherichia coli (E. coli) |
#3: 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: 2.14 Å3/Da / Density % sol: 42.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2M Lithium sulfate monohydrate, 0.1M BIS-TRIS pH 5.5, 25%(w/v) Polyethylene glycol 3,350. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97917 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 30, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97917 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.919→40.26 Å / Num. obs: 24985 / % possible obs: 94.1 % / Redundancy: 6.4 % / Biso Wilson estimate: 25.2 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.07 / Rrim(I) all: 0.18 / Net I/σ(I): 8 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2H5Q, 3K1K Resolution: 1.919→32.554 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.39
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.2 Å2 / Biso mean: 35.3018 Å2 / Biso min: 9.39 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.919→32.554 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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