+Open data
-Basic information
Entry | Database: PDB / ID: 8im1 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | mCherry-LaM1 complex | |||||||||
Components |
| |||||||||
Keywords | FLUORESCENT PROTEIN/IMMUNE SYSTEM / PROTEIN BINDING / FLUORESCENT PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / MCherry fluorescent protein Function and homology information | |||||||||
Biological species | Anaplasma marginale (bacteria) Camelus bactrianus (Bactrian camel) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | |||||||||
Authors | Liang, H. / Liu, R. / Ding, Y. | |||||||||
Funding support | China, 2items
| |||||||||
Citation | Journal: Int J Mol Sci / Year: 2023 Title: Structural Insights into the Binding of Red Fluorescent Protein mCherry-Specific Nanobodies. Authors: Liang, H. / Ma, Z. / Wang, Z. / Zhong, P. / Li, R. / Jiang, H. / Zong, X. / Zhong, C. / Liu, X. / Liu, P. / Liu, J. / Zhu, H. / Liu, R. / Ding, Y. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8im1.cif.gz | 281.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8im1.ent.gz | 228.2 KB | Display | PDB format |
PDBx/mmJSON format | 8im1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8im1_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8im1_full_validation.pdf.gz | 3.5 MB | Display | |
Data in XML | 8im1_validation.xml.gz | 55.1 KB | Display | |
Data in CIF | 8im1_validation.cif.gz | 75.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/im/8im1 ftp://data.pdbj.org/pub/pdb/validation_reports/im/8im1 | HTTPS FTP |
-Related structure data
Related structure data | 8ilxC 8im0C C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 26797.229 Da / Num. of mol.: 4 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 #2: Protein | Mass: 14094.711 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelus bactrianus (Bactrian camel) / Production host: Escherichia coli (E. coli) #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.41 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 0.2 M Potassium sulfate, 20 %(w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Sep 26, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→41.97 Å / Num. obs: 97591 / % possible obs: 96.9 % / Redundancy: 3.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.053 / Rrim(I) all: 0.101 / Χ2: 0.84 / Net I/σ(I): 9 / Num. measured all: 349365 |
Reflection shell | Resolution: 2.05→2.1 Å / % possible obs: 96 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.987 / Num. measured all: 25139 / Num. unique obs: 7164 / CC1/2: 0.54 / Rpim(I) all: 0.619 / Rrim(I) all: 1.169 / Χ2: 0.81 / Net I/σ(I) obs: 1.8 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→32.13 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 1.97 / Phase error: 29.4 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→32.13 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|