+Open data
-Basic information
Entry | Database: PDB / ID: 2vxv | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human IgG ABT-325 Fab Fragment | ||||||
Components | (HUMAN IGG ABT-325) x 2 | ||||||
Keywords | IMMUNE SYSTEM / IL-18 / FAB / TH1/TH2 CELLS / AUTOIMMUNITY | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta Function and homology information | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Argiriadi, M.A. / Xiang, T. / Wu, C. / Ghayur, T. / Borhani, D.W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Unusual Water-Mediated Antigenic Recognition of the Proinflammatory Cytokine Interleukin-18. Authors: Argiriadi, M.A. / Xiang, T. / Wu, C. / Ghayur, T. / Borhani, D.W. | ||||||
History |
| ||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2vxv.cif.gz | 116.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2vxv.ent.gz | 88.3 KB | Display | PDB format |
PDBx/mmJSON format | 2vxv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2vxv_validation.pdf.gz | 451.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2vxv_full_validation.pdf.gz | 453.5 KB | Display | |
Data in XML | 2vxv_validation.xml.gz | 24 KB | Display | |
Data in CIF | 2vxv_validation.cif.gz | 37.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/2vxv ftp://data.pdbj.org/pub/pdb/validation_reports/vx/2vxv | HTTPS FTP |
-Related structure data
Related structure data | 2vxtC 2vxuC 1fnsS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 23946.918 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) Description: ABT-325 IS A RECOMBINANT HUMAN MONOCLONAL ANTIBODY, DERIVED BY IN VITRO SELECTION OF HUMAN IMMUNOGLOBULIN LIBRARIES. Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / Tissue (production host): OVARY |
---|---|
#2: Antibody | Mass: 23518.990 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) Description: ABT-325 IS A RECOMBINANT HUMAN MONOCLONAL ANTIBODY, DERIVED BY IN VITRO SELECTION OF HUMAN IMMUNOGLOBULIN LIBRARIES. Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / Tissue (production host): OVARY |
#3: Chemical | ChemComp-CXS / |
#4: Chemical | ChemComp-GOL / |
#5: 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: 54.1 % / Description: NONE |
---|---|
Crystal grow | Temperature: 277 K / pH: 10.5 Details: ABT-325 FAB FRAGMENT (20 MG/ML, 2 MICROLITERS [UL]) WAS MIXED WITH 2 UL OF A RESERVOIR SOLUTION CONSISTING OF 25 TO 30% POLYETHYLENEGLYCOL (PEG) 400, 100 MM CAPS, PH 10.5 AND SUSPENDED OVER ...Details: ABT-325 FAB FRAGMENT (20 MG/ML, 2 MICROLITERS [UL]) WAS MIXED WITH 2 UL OF A RESERVOIR SOLUTION CONSISTING OF 25 TO 30% POLYETHYLENEGLYCOL (PEG) 400, 100 MM CAPS, PH 10.5 AND SUSPENDED OVER THE RESERVOIR AT 277 K. ROD-LIKE CRYSTALS APPEARED WITHIN ONE DAY. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1.000037 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 29, 2003 / Details: MIRRORS |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000037 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→50 Å / Num. obs: 83126 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.49→1.54 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.1 / % possible all: 92.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FNS Resolution: 1.49→30.71 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.264 / SU ML: 0.042 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.063 / 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: 13.17 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.49→30.71 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|