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- PDB-8hq2: Crystal structure of human ADAM22 in complex with human LGI1 mutant -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hq2 | ||||||
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Title | Crystal structure of human ADAM22 in complex with human LGI1 mutant | ||||||
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![]() | MEMBRANE PROTEIN / SYNAPTIC MODULATOR / COMPLEX | ||||||
Function / homology | ![]() LGI-ADAM interactions / axon initial segment / negative regulation of cell adhesion / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of synaptic transmission / synaptic cleft / central nervous system development / axon guidance / postsynaptic density membrane / metalloendopeptidase activity ...LGI-ADAM interactions / axon initial segment / negative regulation of cell adhesion / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of synaptic transmission / synaptic cleft / central nervous system development / axon guidance / postsynaptic density membrane / metalloendopeptidase activity / neuron projection development / integrin binding / nervous system development / positive regulation of cell growth / cell adhesion / axon / signaling receptor binding / glutamatergic synapse / dendrite / Golgi apparatus / endoplasmic reticulum / proteolysis / extracellular space / extracellular region / membrane / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, H. / Lin, Z. / Xu, F. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of human ADAM22 in complex with human LGI1 mutant Authors: Liu, H. / Lin, Z. / Xu, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 825 KB | Display | ![]() |
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PDB format | ![]() | 683.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 505.2 KB | Display | ![]() |
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Full document | ![]() | 553.9 KB | Display | |
Data in XML | ![]() | 73.4 KB | Display | |
Data in CIF | ![]() | 98.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1w8aS ![]() 3g5cS ![]() 5sxmS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 53743.102 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 60512.379 Da / Num. of mol.: 2 / Mutation: L88N/F89A/R474Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Chemical | ChemComp-CA / #4: Sugar | ChemComp-NAG / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 7.5% PEG 4000, 0.2M MAGNESIUM CHLORIDE, 0.1M HEPES PH=7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 2.93→50 Å / Num. obs: 54802 / % possible obs: 98.4 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.094 / Rsym value: 0.064 / Net I/σ(I): 21.167 |
Reflection shell | Resolution: 2.93→2.99 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.944 / Mean I/σ(I) obs: 2.125 / Num. unique obs: 2716 / Rsym value: 0.694 / % possible all: 97.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1W8A, 5SXM, 3G5C Resolution: 2.93→45.83 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 34.93
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.93→45.83 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: -17.3372 Å / Origin y: -59.4042 Å / Origin z: -63.7304 Å
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Refinement TLS group | Selection details: ALL |