[English] 日本語
Yorodumi- PDB-7cqd: The NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7cqd | ||||||
---|---|---|---|---|---|---|---|
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 | ||||||
Components |
| ||||||
Keywords | HYDROLASE/IMMUNE SYSTEM / soluble domain / Fab complex / MEMBRANE PROTEIN / HYDROLASE-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information 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 / response to hyperoxia / 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-cell adhesion / cell migration / lamellipodium / cell junction / regulation of cell shape / protein-folding chaperone binding / cytoplasmic vesicle / basolateral plasma membrane / cell adhesion / positive regulation of cell migration / membrane raft / apical plasma membrane / 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 | Rattus norvegicus (Norway rat) Aquifex aeolicus VF5 (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å | ||||||
Authors | Tamura-Sakaguchi, R. / Aruga, R. / Nogi, T. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7cqd.cif.gz | 258.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7cqd.ent.gz | 167 KB | Display | PDB format |
PDBx/mmJSON format | 7cqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7cqd_validation.pdf.gz | 475 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7cqd_full_validation.pdf.gz | 487.9 KB | Display | |
Data in XML | 7cqd_validation.xml.gz | 37 KB | Display | |
Data in CIF | 7cqd_validation.cif.gz | 50 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/7cqd ftp://data.pdbj.org/pub/pdb/validation_reports/cq/7cqd | HTTPS FTP |
-Related structure data
Related structure data | 7cqcC 3wklS 4yo0S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
2 |
| ||||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 23409.316 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Mus musculus (house mouse) #2: Antibody | Mass: 23347.764 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Mus musculus (house mouse) #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.) Aquifex aeolicus VF5 (bacteria), (gene. exp.) Homo sapiens (human) Strain: VF5 / Gene: aq_1964 / Production host: Escherichia coli (E. coli) / References: UniProt: O67776, UniProt: Q86YL7 Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.02 Å3/Da / Density % sol: 69.38 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|