[English] 日本語
Yorodumi- PDB-5xcv: Crystal structure of NZ-1 Fv-clasp fragment with its antigen peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xcv | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of NZ-1 Fv-clasp fragment with its antigen peptide | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / antibody fragment / Fv-clasp | ||||||
Function / homology | Function and homology information lymphatic endothelial cell fate commitment / regulation of myofibroblast contraction / actin-mediated cell contraction / leading edge of lamellipodium / lymphangiogenesis / regulation of substrate adhesion-dependent cell spreading / positive regulation of extracellular matrix disassembly / chemokine binding / Specification of primordial germ cells / regulation of lamellipodium morphogenesis ...lymphatic endothelial cell fate commitment / regulation of myofibroblast contraction / actin-mediated cell contraction / leading edge of lamellipodium / lymphangiogenesis / regulation of substrate adhesion-dependent cell spreading / positive regulation of extracellular matrix disassembly / chemokine binding / Specification of primordial germ cells / regulation of lamellipodium morphogenesis / tetraspanin-enriched microdomain / positive regulation of platelet aggregation / filopodium membrane / anchoring junction / wound healing, spreading of cells / microvillus membrane / lamellipodium membrane / Rho protein signal transduction / response to hyperoxia / positive regulation of epithelial to mesenchymal transition / lymph node development / ruffle / GPVI-mediated activation cascade / filopodium / cell projection / lung development / cell-cell adhesion / ruffle membrane / platelet activation / cell migration / lamellipodium / cell junction / regulation of cell shape / protein-folding chaperone binding / cytoplasmic vesicle / basolateral plasma membrane / positive regulation of cell migration / membrane raft / apical plasma membrane / negative regulation of cell population proliferation / signaling receptor binding / negative regulation of apoptotic process / mitochondrion / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Rattus (rat) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.143 Å | ||||||
Authors | Arimori, T. / Takagi, J. | ||||||
Citation | Journal: Structure / Year: 2017 Title: Fv-clasp: An Artificially Designed Small Antibody Fragment with Improved Production Compatibility, Stability, and Crystallizability Authors: Arimori, T. / Kitago, Y. / Umitsu, M. / Fujii, Y. / Asaki, R. / Tamura-Kawakami, K. / Takagi, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5xcv.cif.gz | 281.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5xcv.ent.gz | 229.8 KB | Display | PDB format |
PDBx/mmJSON format | 5xcv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/5xcv ftp://data.pdbj.org/pub/pdb/validation_reports/xc/5xcv | HTTPS FTP |
---|
-Related structure data
Related structure data | 5xcqC 5xcrC 5xcsC 5xctSC 5xcuC 5xcxC 4yo0S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 19370.854 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus (rat), (gene. exp.) Homo sapiens (human) Production host: Escherichia coli (E. coli) #2: Antibody | Mass: 18586.711 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus (rat), (gene. exp.) Homo sapiens (human) Production host: Escherichia coli (E. coli) #3: Protein/peptide | Mass: 1345.432 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q86YL7*PLUS #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.59 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.2M Calcium acetate, 0.1M MES (pH 6.5), 20%(w/v) PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Sep 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.14→50 Å / Num. obs: 46235 / % possible obs: 99.6 % / Redundancy: 4.1 % / Rsym value: 0.109 / Net I/σ(I): 16.05 |
Reflection shell | Resolution: 2.14→2.18 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.39 / Rsym value: 0.674 / % possible all: 99 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5XCT, 4YO0 Resolution: 2.143→41.762 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.36 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.143→41.762 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|