[English] 日本語
Yorodumi- PDB-1yef: STRUCTURE OF IGG2A FAB FRAGMENT (D2.3) COMPLEXED WITH SUBSTRATE A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yef | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURE OF IGG2A FAB FRAGMENT (D2.3) COMPLEXED WITH SUBSTRATE ANALOGUE | ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1yef.cif.gz | 100.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1yef.ent.gz | 78.3 KB | Display | PDB format |
PDBx/mmJSON format | 1yef.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/1yef ftp://data.pdbj.org/pub/pdb/validation_reports/ye/1yef | HTTPS FTP |
---|
-Related structure data
Related structure data | 1yegC 1yehC 1yecS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#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 | ||||||
---|---|---|---|---|---|---|---|
#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 | ||||||
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-PNC / | #5: Water | ChemComp-HOH / | Sequence details | THE SEQUENCES OF THE CONSTANT DOMAINS OF THE HEAVY CHAINS (RESIDUES H 106 - H 223) AND OF THE LIGHT ...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 | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 51.8 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 278 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.94 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 22, 1996 / Details: BENT MIRROR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.94 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 38114 / % possible obs: 98.8 % / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Rsym value: 0.055 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.301 / % possible all: 98.7 |
Reflection | *PLUS Num. measured all: 89942 / Rmerge(I) obs: 0.055 |
Reflection shell | *PLUS % possible obs: 98.7 % / Rmerge(I) obs: 0.301 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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 ELECTRON DENSITY.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 7 Å / Luzzati sigma a obs: 0.27 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→7 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.09 Å / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.84 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|