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- PDB-7cqd: 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: 7cqd | ||||||
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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 235 and 236 | ||||||
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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 | ![]() ![]() ![]() | ||||||
![]() | Tamura-Sakaguchi, R. / Aruga, 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 | ![]() | 258.2 KB | Display | ![]() |
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PDB format | ![]() | 167 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7cqcC ![]() 3wklS ![]() 4yo0S 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 23409.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Antibody | Mass: 23347.764 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein | Mass: 21324.875 Da / Num. of mol.: 2 / Fragment: PDZ tandem fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Strain: VF5 / Gene: aq_1964 / Production host: ![]() ![]() Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.02 Å3/Da / Density % sol: 69.38 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 10%(wt/vol) PEG 3350, 0.2 M L-proline, 0.1 M HEPES-Na (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 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→38.99 Å / Num. obs: 70558 / % possible obs: 99.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 89.12 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.115 / Net I/σ(I): 8 |
Reflection shell | Resolution: 3.2→3.36 Å / Rmerge(I) obs: 0.965 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4745 / CC1/2: 0.774 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4yo0, 3wkl Resolution: 3.2→38.99 Å / SU ML: 0.428 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 33.5126 / 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: 121.44 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→38.99 Å
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Refine LS restraints |
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LS refinement shell |
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