+Open data
-Basic information
Entry | Database: PDB / ID: 1yej | ||||||
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Title | CATALYTIC ANTIBODY COMPLEX | ||||||
Components |
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Keywords | IMMUNE SYSTEM / ABZYME / TRANSITION STATE ANALOG | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Gigant, B. / Knossow, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Crossreactivity, efficiency and catalytic specificity of an esterase-like antibody. 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 | 1yej.cif.gz | 104.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yej.ent.gz | 78.1 KB | Display | PDB format |
PDBx/mmJSON format | 1yej.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/1yej ftp://data.pdbj.org/pub/pdb/validation_reports/ye/1yej | HTTPS FTP |
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-Related structure data
Related structure data | 1yeiC 1yekC 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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Unit cell |
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-Components
#1: Antibody | Mass: 24019.842 Da / Num. of mol.: 1 / Fragment: ANTIGEN BINDING FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: B-LYMPHOCYTE / Strain: BALB/C / References: UniProt: Q58EU8*PLUS | ||||||
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#2: Antibody | Mass: 24189.217 Da / Num. of mol.: 1 / Fragment: ANTIGEN BINDING FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: B-LYMPHOCYTE / Strain: BALB/C | ||||||
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-PNF / | #5: Water | ChemComp-HOH / | Sequence details | THE SEQUENCES OF THE CONSTANT DOMAINS OF THE HEAVY CHAINS. (RESIDUES H106 - H223) AND OF THE LIGHT ...THE SEQUENCES OF THE CONSTANT DOMAINS OF THE HEAVY CHAINS. (RESIDUES H106 - H223) AND OF THE LIGHT CHAINS (RESIDUES L107 - L214) HAVE NOT BEEN DETERMINED | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57 % | |||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: PRECIPITANT: 30% (W/V) PEG 600, 100MM CACODYLATE PH7.5, 40MM ZN ACETATE, VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ | |||||||||||||||||||||||||
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: Jul 12, 1996 / Details: BENT MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→10 Å / Num. obs: 46997 / % possible obs: 96.9 % / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Rsym value: 0.065 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.65 / Rsym value: 0.404 / % possible all: 98.8 |
Reflection | *PLUS Num. measured all: 105615 / Rmerge(I) obs: 0.065 |
Reflection shell | *PLUS % possible obs: 98.8 % / Rmerge(I) obs: 0.404 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YEC Resolution: 1.85→7 Å / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 7 Å / Luzzati sigma a obs: 0.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.93 Å / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 7 Å / σ(F): 2 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.313 / % reflection Rfree: 5 % / Rfactor Rwork: 0.304 / Rfactor obs: 0.304 |