+Open data
-Basic information
Entry | Database: PDB / ID: 1axs | ||||||
---|---|---|---|---|---|---|---|
Title | MATURE OXY-COPE CATALYTIC ANTIBODY WITH HAPTEN | ||||||
Components | (OXY-COPE CATALYTIC ANTIBODY) x 2 | ||||||
Keywords | CATALYTIC ANTIBODY / OXY-COPE / FAB FRAGMENT | ||||||
Function / homology | Function and homology information Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR3A-mediated IL10 synthesis / complement activation, classical pathway / Regulation of Complement cascade / antigen binding / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Mundorff, E.C. / Ulrich, H.D. / Stevens, R.C. | ||||||
Citation | Journal: Nature / Year: 1997 Title: The interplay between binding energy and catalysis in the evolution of a catalytic antibody. Authors: Ulrich, H.D. / Mundorff, E. / Santarsiero, B.D. / Driggers, E.M. / Stevens, R.C. / Schultz, P.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1axs.cif.gz | 180.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1axs.ent.gz | 146.2 KB | Display | PDB format |
PDBx/mmJSON format | 1axs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1axs_validation.pdf.gz | 834.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1axs_full_validation.pdf.gz | 882.5 KB | Display | |
Data in XML | 1axs_validation.xml.gz | 39 KB | Display | |
Data in CIF | 1axs_validation.cif.gz | 53.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/1axs ftp://data.pdbj.org/pub/pdb/validation_reports/ax/1axs | HTTPS FTP |
-Related structure data
Related structure data | 6fabS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||
2 |
| |||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper:
|
-Components
#1: Antibody | Mass: 23529.176 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT Source method: isolated from a genetically manipulated source Details: CHIMERIC FAB FRAGMENT / Source: (gene. exp.) Homo sapiens (human) / Strain: SWISS WEBSTER Description: THE PROTEIN WAS PRODUCED AS CHIMERIC FAB FRAGMENT. THE CONSTANT DOMAINS ARE HUMAN, THE VARIABLE DOMAINS ARE MURINE. PRODUCTION BY EXPRESSION FROM PHOA PROMOTER Cell: B LYMPHOCYTE / Cell line: AZ-28 HYBRIDOMA / Fragment: CHAIN L, A, 108 - 211, CHAIN H, B, 114 - 214 / Organ: SPLEEN / Plasmid: PAZ-28 / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): 25F2 / References: GenBank: 243868, UniProt: Q7Z3Y4*PLUS #2: Antibody | Mass: 23610.342 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT Source method: isolated from a genetically manipulated source Details: CHIMERIC FAB FRAGMENT / Source: (gene. exp.) Homo sapiens (human) / Strain: SWISS WEBSTER Description: THE PROTEIN WAS PRODUCED AS CHIMERIC FAB FRAGMENT. THE CONSTANT DOMAINS ARE HUMAN, THE VARIABLE DOMAINS ARE MURINE. PRODUCTION BY EXPRESSION FROM PHOA PROMOTER Cell: B LYMPHOCYTE / Cell line: AZ-28 HYBRIDOMA / Fragment: CHAIN L, A, 108 - 211, CHAIN H, B, 114 - 214 / Organ: SPLEEN / Plasmid: PAZ-28 / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): 25F2 / References: UniProt: P01857 #3: Chemical | ChemComp-CD / #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 40 % | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 4.6 Details: PROTEIN WAS CRYSTALLIZED FROM 25%PEG 1000, 0.1 M SODIUM ACETATE, PH 4.6, 0.3 M CDCL2 AND 0.1 M AMMONIUM SULFATE IN THE PRESENCE OF 2MM HAPTEN. | ||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 94 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1997 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 24768 / % possible obs: 90.9 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 6 / Rsym value: 0.142 / % possible all: 87.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 6FAB Resolution: 2.6→20 Å / Rfactor Rfree error: 0.0062 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.0001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Weight Biso : 2 / Weight position: 300
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.6→2.72 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|