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Yorodumi- PDB-2jb5: Fab fragment in complex with small molecule hapten, crystal form-1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jb5 | ||||||
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Title | Fab fragment in complex with small molecule hapten, crystal form-1 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / CDR / TSC / FAB / HUCAL / FLUORESCENT DYE / IMMUNOGLOBULIN DOMAIN / ANTIBODY FRAGMENT / DIAGNOSTIC IMAGING | ||||||
Function / homology | Function and homology information IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / IgG immunoglobulin complex / Initial triggering of complement / FCGR activation ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / IgG immunoglobulin complex / Initial triggering of complement / FCGR activation / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / antigen binding / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / Potential therapeutics for SARS / blood microparticle / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Hillig, R.C. / Baesler, S. / Malawski, G. / Badock, V. / Bahr, I. / Schirner, M. / Licha, K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Fab Mor03268 Triggers Absorption Shift of a Diagnostic Dye Via Packaging in a Solvent-Shielded Fab Dimer Interface Authors: Hillig, R.C. / Urlinger, S. / Fanghanel, J. / Brocks, B. / Haenel, C. / Stark, Y. / Sulzle, D. / Svergun, D.I. / Baesler, S. / Malawski, G. / Moosmayer, D. / Menrad, A. / Schirner, M. / Licha, K. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2007 Title: Crystallization and Molecular-Replacement Solution of a Diagnostic Fluorescent Dye in Complex with a Specific Fab Fragment. Authors: Hillig, R.C. / Baesler, S. / Urlinger, S. / Stark, Y. / Bauer, S. / Badock, V. / Huber, M. / Bahr, I. / Schirner, M. / Licha, K. | ||||||
History |
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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 |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jb5.cif.gz | 97.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jb5.ent.gz | 73.3 KB | Display | PDB format |
PDBx/mmJSON format | 2jb5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jb/2jb5 ftp://data.pdbj.org/pub/pdb/validation_reports/jb/2jb5 | HTTPS FTP |
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-Related structure data
Related structure data | 2jb6C 1vgeS C: citing same article (ref.) S: Starting model for refinement |
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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: 26328.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) Description: IN VITRO SELECTED FROM A LIBRARY AND OPTIMIZED IN SEVERAL MATURATION STEPS Production host: ESCHERICHIA COLI (E. coli) |
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#2: Antibody | Mass: 22754.982 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) Description: IN VITRO SELECTED FROM A LIBRARY AND OPTIMIZED IN SEVERAL MATURATION STEPS Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0DOY3*PLUS |
#3: Chemical | ChemComp-T5C / |
#4: Water | ChemComp-HOH / |
Sequence details | HEAVY CHAIN HAS A C-TERMINAL MYC-HIS6 TAG FAB FRAGMENT SELECTED IN VITRO FROM A LIBRARY, AND ...HEAVY CHAIN HAS A C-TERMINAL MYC-HIS6 TAG FAB FRAGMENT SELECTED IN VITRO FROM A LIBRARY, AND OPTIMIZED FURTHER BY MATURATION |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE |
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Crystal grow | pH: 4 Details: 2.3M AMMONIUM SULPHATE, 5% PEG400, 0.1M SODIUM CITRATE PH 4.0, FOR CRYO BUFFER ADITIONAL 15% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 30, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→41.7 Å / Num. obs: 13432 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 61.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2.8→2.85 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.2 / % possible all: 79.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1VGE Resolution: 2.8→41.7 Å / Rfactor Rfree error: 0.011 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE LIGAND TSC IS PARTIALLY DISORDERED. THEREFORE ONLY A FRAGMENT WAS MODELLED. H222-244 REPRESENTS A C-TERMINAL MYC- AND HIS-6 TAG
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.9918 Å2 / ksol: 0.34733 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→41.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.9 Å / Rfactor Rfree error: 0.056 / Total num. of bins used: 10 /
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: LIG_FULL_LINKER.TOP |