+Open data
-Basic information
Entry | Database: PDB / ID: 6j9h | ||||||||||||
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Title | Crystal structure of SVBP-VASH1 complex | ||||||||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN/HYDROLASE / protease / complex / PEPTIDE BINDING PROTEIN / Structural Genomics / Structural Genomics Consortium / SGC / PEPTIDE BINDING PROTEIN-HYDROLASE complex | ||||||||||||
Function / homology | Function and homology information regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / regulation of cellular senescence / Carboxyterminal post-translational modifications of tubulin / negative regulation of lymphangiogenesis / peptidase activator activity / negative regulation of endothelial cell migration / labyrinthine layer blood vessel development / axon development ...regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / regulation of cellular senescence / Carboxyterminal post-translational modifications of tubulin / negative regulation of lymphangiogenesis / peptidase activator activity / negative regulation of endothelial cell migration / labyrinthine layer blood vessel development / 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 / endoplasmic reticulum / proteolysis / extracellular space / extracellular region / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||||||||
Authors | Liao, S. / Gao, J. / Xu, C. / Structural Genomics Consortium (SGC) | ||||||||||||
Funding support | China, 3items
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Citation | Journal: Cell Res. / Year: 2019 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j9h.cif.gz | 230 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j9h.ent.gz | 184.1 KB | Display | PDB format |
PDBx/mmJSON format | 6j9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/6j9h ftp://data.pdbj.org/pub/pdb/validation_reports/j9/6j9h | HTTPS FTP |
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-Related structure data
Related structure data | 6j7bC 6j8fC 6j8nC 6j91SC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-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: 7821.939 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SVBP, CCDC23 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q8N300 #2: Protein | Mass: 27668.096 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: VASH1, KIAA1036, VASH Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q7L8A9, tubulinyl-Tyr carboxypeptidase #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.51 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1M Na citrate tribasic dihydrate pH 5.5, 16% PEG 8000, 0.01M Cadmium chloride hydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 9, 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: 2.31→75.03 Å / Num. obs: 37912 / % possible obs: 99.9 % / Redundancy: 12.6 % / Rpim(I) all: 0.075 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.31→2.43 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 3.4 / Num. unique obs: 5413 / CC1/2: 0.895 / Rpim(I) all: 0.428 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6J91 Resolution: 2.31→62.201 Å / SU ML: 0.24 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 31.67
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.31→62.201 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: -0.1665 Å / Origin y: -10.0602 Å / Origin z: -32.9116 Å
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Refinement TLS group | Selection details: all |