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- PDB-7cqc: The NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7cqc | |||||||||
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Title | The NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicus S2P homolog with the PA14 tag inserted between the residues 181 and 184 | |||||||||
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![]() | HYDROLASE/IMMUNE SYSTEM / soluble domain / Fab complex / Membrane protein / HYDROLASE-IMMUNE SYSTEM complex | |||||||||
Function / homology | ![]() lymphatic endothelial cell fate commitment / regulation of myofibroblast contraction / actin-mediated cell contraction / leading edge of lamellipodium / regulation of substrate adhesion-dependent cell spreading / positive regulation of extracellular matrix disassembly / chemokine binding / Specification of primordial germ cells / lymphangiogenesis / regulation of lamellipodium morphogenesis ...lymphatic endothelial cell fate commitment / regulation of myofibroblast contraction / actin-mediated cell contraction / leading edge of lamellipodium / regulation of substrate adhesion-dependent cell spreading / positive regulation of extracellular matrix disassembly / chemokine binding / Specification of primordial germ cells / lymphangiogenesis / regulation of lamellipodium morphogenesis / tetraspanin-enriched microdomain / positive regulation of platelet aggregation / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / filopodium membrane / anchoring junction / wound healing, spreading of cells / microvillus membrane / lamellipodium membrane / Rho protein signal transduction / lymph node development / positive regulation of epithelial to mesenchymal transition / GPVI-mediated activation cascade / ruffle / filopodium / cell projection / lung development / platelet activation / metalloendopeptidase activity / ruffle membrane / cell migration / cell junction / lamellipodium / protein-folding chaperone binding / regulation of cell shape / cytoplasmic vesicle / basolateral plasma membrane / cell adhesion / positive regulation of cell migration / apical plasma membrane / membrane raft / negative regulation of cell population proliferation / signaling receptor binding / negative regulation of apoptotic process / signal transduction / mitochondrion / proteolysis / membrane / metal ion binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Aruga, R. / Tamura-Sakaguchi, R. / Nogi, T. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Moving toward generalizable NZ-1 labeling for 3D structure determination with optimized epitope-tag insertion. Authors: Tamura-Sakaguchi, R. / Aruga, R. / Hirose, M. / Ekimoto, T. / Miyake, T. / Hizukuri, Y. / Oi, R. / Kaneko, M.K. / Kato, Y. / Akiyama, Y. / Ikeguchi, M. / Iwasaki, K. / Nogi, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 161.6 KB | Display | ![]() |
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PDB format | ![]() | 101.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7cqdC ![]() 3wklS ![]() 4yooS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 23409.316 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 23347.764 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 21135.703 Da / Num. of mol.: 1 / Fragment: PDZ tandem fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: VF5 / Gene: aq_1964 / Production host: ![]() ![]() |
#4: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.55 Å3/Da / Density % sol: 51.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 20%(wt./vol.) PEG 3350, 0.2 M potassium sodium tartrate |
-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: Mar 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→45.68 Å / Num. obs: 47746 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 59.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.5→2.6 Å / Rmerge(I) obs: 1.469 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2685 / CC1/2: 0.674 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4yoO, 3wkl Resolution: 2.5→42.97 Å / SU ML: 0.4623 / Cross valid method: FREE R-VALUE / σ(F): 0.09 / Phase error: 34.1829 / Stereochemistry target values: GeoStd + Monomer Library Details: the entry contains Friedel pairs in F_Plus/Minus columns
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→42.97 Å
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Refine LS restraints |
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LS refinement shell |
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