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Yorodumi- PDB-1aj7: IMMUNOGLOBULIN 48G7 GERMLINE FAB ANTIBODY COMPLEXED WITH HAPTEN 5... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1aj7 | ||||||
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Title | IMMUNOGLOBULIN 48G7 GERMLINE FAB ANTIBODY COMPLEXED WITH HAPTEN 5-(PARA-NITROPHENYL PHOSPHONATE)-PENTANOIC ACID. AFFINITY MATURATION OF AN ESTEROLYTIC ANTIBODY | ||||||
Components |
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Keywords | IMMUNOGLOBULIN / GERMLINE ANTIBODY / FAB / CATALYTIC ANTIBODY / AFFINITY MATURATION | ||||||
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 / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis ...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 / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis / complement activation, classical pathway / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / 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 / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Wedemayer, G.J. / Wang, L.H. / Patten, P.A. / Schultz, P.G. / Stevens, R.C. | ||||||
Citation | Journal: Science / Year: 1997 Title: Structural insights into the evolution of an antibody combining site. Authors: Wedemayer, G.J. / Patten, P.A. / Wang, L.H. / Schultz, P.G. / Stevens, R.C. #1: Journal: J.Mol.Biol. / Year: 1997 Title: Crystal Structures of the Free and Liganded Form of an Esterolytic Catalytic Antibody Authors: Wedemayer, G.J. / Wang, L.H. / Patten, P.A. / Schultz, P.G. / Stevens, R.C. #2: Journal: Science / Year: 1996 Title: The Immunological Evolution of Catalysis Authors: Patten, P.A. / Gray, N.S. / Yang, P.L. / Marks, C.B. / Wedemayer, G.J. / Boniface, J.J. / Stevens, R.C. / Schultz, P.G. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993 Title: A Genetic Approach to the Generation of Antibodies with Enhanced Catalytic Activities Authors: Lesley, S.A. / Patten, P.A. / Schultz, P.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1aj7.cif.gz | 110.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aj7.ent.gz | 84.7 KB | Display | PDB format |
PDBx/mmJSON format | 1aj7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1aj7_validation.pdf.gz | 696.5 KB | Display | wwPDB validaton report |
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Full document | 1aj7_full_validation.pdf.gz | 700.6 KB | Display | |
Data in XML | 1aj7_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 1aj7_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/1aj7 ftp://data.pdbj.org/pub/pdb/validation_reports/aj/1aj7 | HTTPS FTP |
-Related structure data
Related structure data | 2rcsC 1gafS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Antibody | Mass: 23464.988 Da / Num. of mol.: 1 Fragment: VARIABLE DOMAINS OF LIGHT AND HEAVY CHAINS AND CONSTANT DOMAINS OF LIGHT AND HEAVY CHAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) Description: EACH CHAIN IS A FUSION POLYPEPTIDE WHICH IS PART HUMAN AND PART MOUSE Cell line: 48G7 / Fragment: CONSTANT DOMAINS OF LIGHT AND HEAVY CHAINS / Plasmid: PSAL143 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 4768677 |
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#2: Antibody | Mass: 23062.750 Da / Num. of mol.: 1 Fragment: VARIABLE DOMAINS OF LIGHT AND HEAVY CHAINS AND CONSTANT DOMAINS OF LIGHT AND HEAVY CHAINS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Description: EACH CHAIN IS A FUSION POLYPEPTIDE WHICH IS PART HUMAN AND PART MOUSE Cell line: 48G7 / Fragment: CONSTANT DOMAINS OF LIGHT AND HEAVY CHAINS / Plasmid: PSAL143 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01857 |
#3: Chemical | ChemComp-NPE / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.29 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 Details: 10-15 MG/ML FAB IN 100MM NACL, 10MM TRIS PH 8.0, 1MM METHIONINE, 1MM SODIUM AZIDE, 0.5 MM EDTA. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1996 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 23005 / % possible obs: 99.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.1→2.17 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 5.2 / Rsym value: 0.204 / % possible all: 98.1 |
Reflection | *PLUS Num. measured all: 80267 |
Reflection shell | *PLUS % possible obs: 98.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GAF Resolution: 2.1→20 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.11 Å / Total num. of bins used: 60
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