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Yorodumi- PDB-1nd0: CATIONIC CYCLIZATION ANTIBODY 4C6 COMPLEX WITH TRANSITION STATE ANALOG -
+Open data
-Basic information
Entry | Database: PDB / ID: 1nd0 | ||||||
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Title | CATIONIC CYCLIZATION ANTIBODY 4C6 COMPLEX WITH TRANSITION STATE ANALOG | ||||||
Components | (IMMUNOGLOBULIN IGG2A) x 2 | ||||||
Keywords | IMMUNE SYSTEM / Immunoglobulin / catalytic antibody / cationic cyclization reaction | ||||||
Function / homology | Function and homology information positive regulation of B cell activation / humoral immune response mediated by circulating immunoglobulin / early endosome to late endosome transport / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / endosome to lysosome transport / phagocytosis, engulfment ...positive regulation of B cell activation / humoral immune response mediated by circulating immunoglobulin / early endosome to late endosome transport / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / endosome to lysosome transport / phagocytosis, engulfment / positive regulation of endocytosis / antigen processing and presentation / immunoglobulin mediated immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / positive regulation of phagocytosis / multivesicular body / complement activation, classical pathway / antigen binding / response to bacterium / positive regulation of immune response / antibacterial humoral response / immune 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: 2.45 Å | ||||||
Authors | Zhu, X. / Wilson, I.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Structural Basis for Antibody Catalysis of a Cationic Cyclization Reaction Authors: Zhu, X. / Heine, A. / Monnat, F. / Houk, K.N. / Janda, K.D. / Wilson, I.A. | ||||||
History |
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Remark 999 | SEQUENCE AN APPROPRIATE SEQUENCE DATABASE REFERENCE WAS NOT AVAILABLE AT THE TIME OF PROCESSING. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nd0.cif.gz | 349.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nd0.ent.gz | 284.5 KB | Display | PDB format |
PDBx/mmJSON format | 1nd0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nd0_validation.pdf.gz | 514.5 KB | Display | wwPDB validaton report |
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Full document | 1nd0_full_validation.pdf.gz | 560.8 KB | Display | |
Data in XML | 1nd0_validation.xml.gz | 70.3 KB | Display | |
Data in CIF | 1nd0_validation.cif.gz | 94.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/1nd0 ftp://data.pdbj.org/pub/pdb/validation_reports/nd/1nd0 | HTTPS FTP |
-Related structure data
Related structure data | 1ncwSC 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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Unit cell |
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-Components
#1: Antibody | Mass: 24219.010 Da / Num. of mol.: 4 / Fragment: IMMUNOGLOBULIN FAB FRAGMENT, light chain / Source method: isolated from a natural source / Details: Purified from Ascitic fluid / Source: (natural) Mus musculus (house mouse) / Strain: 129G1X+ / References: UniProt: Q8K0F8, UniProt: Q58EU8*PLUS #2: Antibody | Mass: 23816.590 Da / Num. of mol.: 4 / Fragment: IMMUNOGLOBULIN FAB FRAGMENT, heavy chain / Source method: isolated from a natural source / Details: Purified from Ascitic fluid / Source: (natural) Mus musculus (house mouse) / Strain: 129G1X+ / References: UniProt: P01865 #3: Chemical | ChemComp-DP4 / ( #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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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: 2.42 Å3/Da / Density % sol: 48.86 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: evaporation / pH: 5.5 Details: ammonium sulfate, dioxane, tri-sodium citrate dihydrate, pH 5.5, evaporation, temperature 295K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 4, 2001 |
Radiation | Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. all: 67638 / Num. obs: 53415 / % possible obs: 79.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.45→2.49 Å / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 1.5 / % possible all: 78.4 |
Reflection | *PLUS Lowest resolution: 50 Å / Redundancy: 1.7 % |
Reflection shell | *PLUS % possible obs: 78.4 % / Redundancy: 1.7 % / Num. unique obs: 2598 / Mean I/σ(I) obs: 1.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NCW Resolution: 2.45→50 Å / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 35 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→50 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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