+Open data
-Basic information
Entry | Database: PDB / ID: 3m8o | ||||||
---|---|---|---|---|---|---|---|
Title | Human IgA1 Fab fragment | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / Immunoglobulin fold | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / ML / Resolution: 1.55 Å | ||||||
Authors | Buschiazzo, A. / Trajtenberg, F. / Correa, A. / Oppezzo, P. / Pritsch, O. / Dighiero, G. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2013 Title: Structure of a human IgA1 Fab fragment at 1.55 angstrom resolution: potential effect of the constant domains on antigen-affinity modulation Authors: Correa, A. / Trajtenberg, F. / Obal, G. / Pritsch, O. / Dighiero, G. / Oppezzo, P. / Buschiazzo, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3m8o.cif.gz | 200 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3m8o.ent.gz | 157.8 KB | Display | PDB format |
PDBx/mmJSON format | 3m8o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m8/3m8o ftp://data.pdbj.org/pub/pdb/validation_reports/m8/3m8o | HTTPS FTP |
---|
-Related structure data
Related structure data | 3qnxC 3qnySC 3qnzC 3qo1C C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 24009.725 Da / Num. of mol.: 1 / Fragment: Fab fragment / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) | ||||
---|---|---|---|---|---|
#2: Antibody | Mass: 23506.275 Da / Num. of mol.: 1 / Fragment: Fab fragment / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) | ||||
#3: Chemical | ChemComp-CL / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.89 Å3/Da / Density % sol: 34.99 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 30% PEG 3000, 0.2M sodium chloride, 0.1M tris, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 108 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 19, 2008 / Details: Varimax HF mirrors |
Radiation | Monochromator: Varimax HF mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→20 Å / Num. all: 50274 / Num. obs: 50274 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.34 % / Biso Wilson estimate: 19.987 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 19.51 |
Reflection shell | Resolution: 1.55→1.59 Å / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 6.8 / Num. measured obs: 9617 / Num. unique obs: 3314 / % possible all: 88 |
-Phasing
Phasing | Method: ML |
---|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3QNY Resolution: 1.55→19.289 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9 / SU ML: 0.16 / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: ML Details: HYDROGENS HAVE BEEN ADDED IN RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.489 Å2 / ksol: 0.37 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 55.22 Å2 / Biso mean: 16.098 Å2 / Biso min: 3.34 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→19.289 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|