+Open data
-Basic information
Entry | Database: PDB / ID: 3eak | ||||||
---|---|---|---|---|---|---|---|
Title | NbBCII10 humanized (FGLA mutant) | ||||||
Components | NbBCII10-FGLA | ||||||
Keywords | IMMUNE SYSTEM / antibody / nanobody / humanization / VHH domain | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Camelus dromedarius (Arabian camel) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Vincke, C. / Loris, R. / Saerens, D. / Martinez-Rodriguez, S. / Muyldermans, S. / Conrath, K. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: General strategy to humanize a camelid single-domain antibody and identification of a universal humanized nanobody scaffold. Authors: Vincke, C. / Loris, R. / Saerens, D. / Martinez-Rodriguez, S. / Muyldermans, S. / Conrath, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3eak.cif.gz | 64.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3eak.ent.gz | 47 KB | Display | PDB format |
PDBx/mmJSON format | 3eak.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3eak_validation.pdf.gz | 440.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3eak_full_validation.pdf.gz | 445.2 KB | Display | |
Data in XML | 3eak_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 3eak_validation.cif.gz | 20 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/3eak ftp://data.pdbj.org/pub/pdb/validation_reports/ea/3eak | HTTPS FTP |
-Related structure data
Related structure data | 3dwtC 3ebaC 1zmyS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
2 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-Components
#1: Antibody | Mass: 14985.692 Da / Num. of mol.: 2 Mutation: S11L, A14P, T23A, E47G, R48L, A78S, V82L, T83Y, N88S, K90R, P91A, I96V, Q123L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Plasmid: pHEN6 / Production host: Escherichia coli (E. coli) / Strain (production host): WK5 #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | Sequence details | THERE ARE 13 MUTATIONS S11L, A14P, T23A, E47G, R48L, A78S, V82L, T83Y, N88S, K90R, P91A, I96V, Q123L | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.26 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100mM Na-Hepes pH 7.5, 2% PEG 400, 2M NH4(SO4)2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.909 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 1, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.909 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→50 Å / Num. all: 20171 / Num. obs: 20171 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.196 / Rsym value: 0.196 / Net I/σ(I): 9.99 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.607 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1998 / Rsym value: 0.607 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1zmy Resolution: 1.95→50 Å / Isotropic thermal model: individual isotropic B-factors / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: used mli target in cns including global anisotropic b-factor correction and bulk solvent correction
| |||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→50 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|