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Open data
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Basic information
Entry | Database: PDB / ID: 6j8n | ||||||||||||
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Title | Crystal structure of SVBP-VASH1 complex, mutation C169A of VASH1 | ||||||||||||
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![]() | PEPTIDE BINDING PROTEIN/HYDROLASE / protease / complex / PEPTIDE BINDING PROTEIN / PEPTIDE BINDING PROTEIN-HYDROLASE complex / Structural Genomics / Structural Genomics Consortium / SGC | ||||||||||||
Function / homology | ![]() regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / Carboxyterminal post-translational modifications of tubulin / regulation of cellular senescence / negative regulation of lymphangiogenesis / peptidase activator activity / labyrinthine layer blood vessel development / negative regulation of endothelial cell migration / axon development ...regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / Carboxyterminal post-translational modifications of tubulin / regulation of cellular senescence / negative regulation of lymphangiogenesis / peptidase activator activity / labyrinthine layer blood vessel development / negative regulation of endothelial cell migration / axon development / negative regulation of endothelial cell proliferation / negative regulation of blood vessel endothelial cell migration / protein secretion / regulation of angiogenesis / metallocarboxypeptidase activity / negative regulation of protein ubiquitination / negative regulation of angiogenesis / response to wounding / apical part of cell / actin binding / microtubule binding / angiogenesis / cytoskeleton / regulation of cell cycle / cell cycle / endoplasmic reticulum / proteolysis / extracellular space / extracellular region / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Liao, S. / Gao, J. / Xu, C. / Structural Genomics Consortium (SGC) | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Molecular basis of vasohibins-mediated detyrosination and its impact on spindle function and mitosis. Authors: Liao, S. / Rajendraprasad, G. / Wang, N. / Eibes, S. / Gao, J. / Yu, H. / Wu, G. / Tu, X. / Huang, H. / Barisic, M. / Xu, C. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.3 KB | Display | ![]() |
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PDB format | ![]() | 103 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 442.4 KB | Display | ![]() |
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Full document | ![]() | 447.5 KB | Display | |
Data in XML | ![]() | 27.7 KB | Display | |
Data in CIF | ![]() | 41.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6j7bC ![]() 6j8fC ![]() 6j91C ![]() 6j9hC C: citing same article ( |
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Similar structure data | |
Other databases |
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Links
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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: 7821.939 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: Q8N300 #2: Protein | Mass: 27636.031 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() References: UniProt: Q7L8A9, tubulinyl-Tyr carboxypeptidase #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.57 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 6% v/v Tacsimate pH6.0, 0.1M MES monohydrate pH 6.0, 25% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. obs: 58570 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 1 / Rpim(I) all: 0.048 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 12.6 % / Num. unique obs: 5755 / Rpim(I) all: 0.292 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: a low resolution SeMet structure in our group Resolution: 1.95→33.703 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 20.95
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→33.703 Å
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Refine LS restraints |
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LS refinement shell |
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