[English] 日本語
Yorodumi- PDB-5d7s: Crystal structure of MOR04357, a neutralizing anti-human GM-CSF a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d7s | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of MOR04357, a neutralizing anti-human GM-CSF antibody Fab fragment | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / GM-CSF / affinity maturation / phage display / cytokine / antibody / PROTEROS BIOSTRUCTURES GMBH | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / (2S,3S)-butane-2,3-diol Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å | ||||||
Authors | Eylenstein, R. / Weinfurtner, D. / Steidl, S. / Boettcher, J. / Augustin, M. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: Mabs / Year: 2016 Title: Molecular basis of in vitro affinity maturation and functional evolution of a neutralizing anti-human GM-CSF antibody. Authors: Eylenstein, R. / Weinfurtner, D. / Hartle, S. / Strohner, R. / Bottcher, J. / Augustin, M. / Ostendorp, R. / Steidl, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5d7s.cif.gz | 174.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5d7s.ent.gz | 143.2 KB | Display | PDB format |
PDBx/mmJSON format | 5d7s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d7s_validation.pdf.gz | 453.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5d7s_full_validation.pdf.gz | 458.3 KB | Display | |
Data in XML | 5d7s_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 5d7s_validation.cif.gz | 27 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/5d7s ftp://data.pdbj.org/pub/pdb/validation_reports/d7/5d7s | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 22229.715 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: 25458.283 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) | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.25 Details: 26 % PEG3350, 0.2 M NaCl and 0.1 M Tris, pH 8.25, 10.5 mg/mL protein |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å | |||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 11, 2011 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 1.88→78.33 Å / Num. obs: 36714 / % possible obs: 97.8 % / Observed criterion σ(I): 0 / Redundancy: 7.9 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 14.17 | |||||||||
Reflection shell | Resolution: 1.88→2 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.618 / % possible all: 96.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→78.33 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.925 / SU B: 8.638 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.282 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.88→78.33 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|