+Open data
-Basic information
Entry | Database: PDB / ID: 3b9v | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of an Autonomous VH Domain | ||||||
Components | heavy chain variable domain | ||||||
Keywords | IMMUNE SYSTEM / antibody engineering / phage display | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Appleton, B.A. / Barthelemy, P.A. / Wiesmann, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2008 Title: Comprehensive Analysis of the Factors Contributing to the Stability and Solubility of Autonomous Human VH Domains. Authors: Barthelemy, P.A. / Raab, H. / Appleton, B.A. / Bond, C.J. / Wu, P. / Wiesmann, C. / Sidhu, S.S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3b9v.cif.gz | 111.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3b9v.ent.gz | 85.6 KB | Display | PDB format |
PDBx/mmJSON format | 3b9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3b9v_validation.pdf.gz | 431.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3b9v_full_validation.pdf.gz | 433.2 KB | Display | |
Data in XML | 3b9v_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 3b9v_validation.cif.gz | 33.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/3b9v ftp://data.pdbj.org/pub/pdb/validation_reports/b9/3b9v | HTTPS FTP |
-Related structure data
Related structure data | 1n8zS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 13054.447 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45 % |
---|---|
Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 1.1 M sodium malonate, 0.1 M Hepes, 0.5% Jeffamine ED-2001, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 40233 / % possible obs: 96.2 % / Redundancy: 4 % / Rsym value: 0.039 / Χ2: 1.326 / Net I/σ(I): 43.2 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4 % / Mean I/σ(I) obs: 13.4 / Num. unique all: 3886 / Rsym value: 0.097 / Χ2: 0.882 / % possible all: 92.6 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1N8Z Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.358 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.121 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.485 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.8→1.837 Å / Total num. of bins used: 25
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|