+Open data
-Basic information
Entry | Database: PDB / ID: 1kn4 | ||||||
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Title | CATALYTIC ANTIBODY D2.3 COMPLEX | ||||||
Components |
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Keywords | IMMUNE SYSTEM / ABZYME / TRANSITION STATE ANALOG | ||||||
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 / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Gigant, B. / Knossow, M. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2002 Title: Remarkable remote chiral recognition in a reaction mediated by a catalytic antibody. Authors: D'Souza, L.J. / Gigant, B. / Knossow, M. / Green, B.S. | ||||||
History |
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Remark 600 | HETEROGEN PDE IS PARA-NITROPHENYL PHOSPHONOBUTANOYL D-ALANINE (NO2-C6H5-O-PO2-CH2-CH2-CH2-CO-NH-CH(CH3)-COOH) | ||||||
Remark 999 | SEQUENCE THE SEQUENCES OF THE CONSTANT DOMAINS OF THE HEAVY CHAINS. (RESIDUES H106 - H223) AND OF ...SEQUENCE 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 FOR THIS IMMUNOGLOBULIN. THEY HAVE BEEN ASSIGNED THE CONSENSUS SEQUENCE FOR THE CONSTANT DOMAIN OF MOUSE KAPPA LIGHT CHAIN AND FOR THE FIRST CONSTANT DOMAIN OF MOUSE GROUP 2A HEAVY CHAINS. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1kn4.cif.gz | 104.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1kn4.ent.gz | 78 KB | Display | PDB format |
PDBx/mmJSON format | 1kn4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kn/1kn4 ftp://data.pdbj.org/pub/pdb/validation_reports/kn/1kn4 | HTTPS FTP |
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-Related structure data
Related structure data | 1kn2C 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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3 |
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4 |
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Unit cell |
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-Components
#1: Antibody | Mass: 24019.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8K0F8, UniProt: Q58EU8*PLUS | ||||
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#2: Antibody | Mass: 24189.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01863*PLUS | ||||
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-PDE / | #5: Water | ChemComp-HOH / | |
-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 Details: PEG600, ZnSO4, Cacodylate, pH 7.00, VAPOR DIFFUSION, HANGING DROP | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.5 / Details: Gigant, B., (1998) J. Mol. Biol., 284, 741. | |||||||||||||||||||||||||
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: 0.963 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 8, 1998 / Details: BENT MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.963 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 43212 / Num. obs: 43212 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 23.8 Å2 / Rsym value: 0.07 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.9→1.93 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.0439 / % possible all: 97.6 |
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Num. obs: 42817 / % possible obs: 94.7 % / Num. measured all: 106350 / Rmerge(I) obs: 0.085 |
Reflection shell | *PLUS % possible obs: 98.2 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 3.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1YEC Resolution: 1.9→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1811954.89 / Data cutoff high rms absF: 1811954.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 31.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.99 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 8
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Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.213 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 31.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS % reflection Rfree: 5.2 % / Rfactor Rwork: 0.275 / Rfactor obs: 0.275 |