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Yorodumi- PDB-1yeg: STRUCTURE OF IGG2A FAB FRAGMENT (D2.3) COMPLEXED WITH REACTION PRODUCT -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yeg | ||||||
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Title | STRUCTURE OF IGG2A FAB FRAGMENT (D2.3) COMPLEXED WITH REACTION PRODUCT | ||||||
Components | (IGG2A FAB FRAGMENT) x 2 | ||||||
Keywords | CATALYTIC ANTIBODY | ||||||
Function / homology | Function and homology information Fc-gamma receptor I complex binding / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / extracellular space / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Gigant, B. / Knossow, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1997 Title: X-ray structures of a hydrolytic antibody and of complexes elucidate catalytic pathway from substrate binding and transition state stabilization through water attack and product release. Authors: Gigant, B. / Charbonnier, J.B. / Eshhar, Z. / Green, B.S. / Knossow, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yeg.cif.gz | 100.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yeg.ent.gz | 78.1 KB | Display | PDB format |
PDBx/mmJSON format | 1yeg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/1yeg ftp://data.pdbj.org/pub/pdb/validation_reports/ye/1yeg | HTTPS FTP |
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-Related structure data
Related structure data | 1yefC 1yehC 1yecS 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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2 |
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Unit cell |
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-Components
-Antibody , 2 types, 2 molecules LH
#1: Antibody | Mass: 24005.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: STRUCTURE OF IGG2A FAB FRAGMENT (D2.3) / Source: (natural) Mus musculus (house mouse) / References: PIR: S16112 |
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#2: Antibody | Mass: 24189.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: STRUCTURE OF IGG2A FAB FRAGMENT (D2.3) / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01863 |
-Non-polymers , 4 types, 163 molecules
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-BPN / | #5: Chemical | ChemComp-ACT / | #6: Water | ChemComp-HOH / | |
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-Details
Sequence details | THE SEQUENCES OF THE CONSTANT DOMAINS OF THE HEAVY CHAINS. (RESIDUES H 106 - H 223) AND OF THE ...THE SEQUENCES OF THE CONSTANT DOMAINS OF THE HEAVY CHAINS. (RESIDUES H 106 - H 223) AND OF THE LIGHT CHAINS (RESIDUES L 107 - L 214) HAVE NOT BEEN DETERMINED |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 52.5 % | |||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: HANGING DROP METHOD. PRECIPITANT: 30% (W/V) PEG 600, 100MM CACODYLATE PH7.5, 40MM ZN ACETATE., vapor diffusion - hanging drop | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 278 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 19, 1996 / Details: BENT MIRROR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2→17 Å / Num. obs: 39071 / % possible obs: 99.6 % / Observed criterion σ(I): 1 / Redundancy: 2.5 % / Rsym value: 0.052 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.313 / % possible all: 98.6 |
Reflection | *PLUS Num. measured all: 98164 / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS % possible obs: 98.6 % / Rmerge(I) obs: 0.313 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1YEC Resolution: 2→7 Å / σ(F): 2 Details: RESIDUES 212 - 214 OF THE LIGHT CHAIN AND 127 - 134 OF THE HEAVY CHAIN ARE POORLY DEFINED BY THE
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Displacement parameters | Biso mean: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 7 Å / Luzzati sigma a obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.09 Å / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 3.84 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.24 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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