+Open data
-Basic information
Entry | Database: PDB / ID: 6j8o | ||||||||||||
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Title | Structure of a hypothetical protease | ||||||||||||
Components |
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Keywords | PEPTIDE BINDING PROTEIN/HYDROLASE / protease / complex / PEPTIDE BINDING PROTEIN / PEPTIDE BINDING PROTEIN-HYDROLASE complex | ||||||||||||
Function / homology | Function and homology information regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / Post-chaperonin tubulin folding pathway / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / regulation of cellular senescence / negative regulation of lymphangiogenesis / peptidase activator activity ...regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / Post-chaperonin tubulin folding pathway / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / regulation of cellular senescence / negative regulation of lymphangiogenesis / peptidase activator activity / cytoskeleton-dependent intracellular transport / Intraflagellar transport / Sealing of the nuclear envelope (NE) by ESCRT-III / Gap junction assembly / Formation of tubulin folding intermediates by CCT/TriC / COPI-independent Golgi-to-ER retrograde traffic / Kinesins / Assembly and cell surface presentation of NMDA receptors / COPI-dependent Golgi-to-ER retrograde traffic / labyrinthine layer blood vessel development / negative regulation of endothelial cell migration / axon development / Recycling pathway of L1 / negative regulation of endothelial cell proliferation / RHOH GTPase cycle / negative regulation of blood vessel endothelial cell migration / protein secretion / RHO GTPases activate IQGAPs / Hedgehog 'off' state / regulation of angiogenesis / cytoplasmic microtubule / metallocarboxypeptidase activity / microtubule-based process / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / negative regulation of protein ubiquitination / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / cellular response to interleukin-4 / negative regulation of angiogenesis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / PKR-mediated signaling / structural constituent of cytoskeleton / microtubule cytoskeleton organization / Aggrephagy / response to wounding / HCMV Early Events / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / double-stranded RNA binding / apical part of cell / mitotic cell cycle / actin binding / microtubule binding / angiogenesis / microtubule / cytoskeleton / regulation of cell cycle / cell cycle / cell division / GTPase activity / ubiquitin protein ligase binding / GTP binding / structural molecule activity / endoplasmic reticulum / proteolysis / extracellular space / extracellular region / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.855 Å | ||||||||||||
Authors | Liao, S. / Gao, J. / Xu, C. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: To Be Published Title: Structure of a hypothetical protease Authors: Liao, S. / Gao, J. / Xu, C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6j8o.cif.gz | 79.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6j8o.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 6j8o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/6j8o ftp://data.pdbj.org/pub/pdb/validation_reports/j8/6j8o | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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/peptide | Mass: 5667.565 Da / Num. of mol.: 1 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 |
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#2: Protein | Mass: 27652.031 Da / Num. of mol.: 1 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: Protein/peptide | Mass: 940.862 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68363*PLUS |
#4: 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: 2.87 Å3/Da / Density % sol: 57.11 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1M BIS-TRIS pH 6.5, 16% polyethylene glycol 10000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9785 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 34141 / % possible obs: 99.9 % / Redundancy: 8.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.031 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 8 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3364 / CC1/2: 0.739 / Rpim(I) all: 0.315 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: a low resolution SeMet structure from our group Resolution: 1.855→44.31 Å / SU ML: 0.16 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 18.59
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.855→44.31 Å
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Refine LS restraints |
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LS refinement shell |
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