[English] 日本語
Yorodumi- PDB-6dw2: Structure of the 6078 Antibody Fab fragment bound to a Staphyloco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dw2 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of the 6078 Antibody Fab fragment bound to a Staphylococcus aureus wall techoic acid analog | |||||||||
Components |
| |||||||||
Keywords | IMMUNE SYSTEM / Antibody / Fab / wall teichoic acid / WTA / Staphylococcus aureus | |||||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-HD4 / MALONIC ACID Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Fong, R. / Lupardus, P.J. | |||||||||
Citation | Journal: MAbs / Year: 2018 Title: Structural investigation of human S. aureus-targeting antibodies that bind wall teichoic acid. Authors: Fong, R. / Kajihara, K. / Chen, M. / Hotzel, I. / Mariathasan, S. / Hazenbos, W.L.W. / Lupardus, P.J. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6dw2.cif.gz | 113.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6dw2.ent.gz | 82.2 KB | Display | PDB format |
PDBx/mmJSON format | 6dw2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/6dw2 ftp://data.pdbj.org/pub/pdb/validation_reports/dw/6dw2 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6dwaC 6dwcC 6dwiC 4kvnS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Antibody , 2 types, 2 molecules AB
#1: Antibody | Mass: 26023.232 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
---|---|
#2: Antibody | Mass: 27135.594 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) |
-Sugars , 1 types, 1 molecules
#5: Sugar | ChemComp-HD4 / |
---|
-Non-polymers , 3 types, 409 molecules
#3: Chemical | #4: Chemical | ChemComp-MLA / | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.45 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / Details: 1.9 M sodium malonate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 7, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 64097 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 28.07 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 30.4 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 6316 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KVN Resolution: 1.7→45.55 Å / Cor.coef. Fo:Fc: 0.9602 / Cor.coef. Fo:Fc free: 0.9495 / SU R Cruickshank DPI: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.094 / SU Rfree Blow DPI: 0.089 / SU Rfree Cruickshank DPI: 0.086
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.39 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.221 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.7→45.55 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.74 Å / Total num. of bins used: 20
|