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- PDB-1ruk: Crystal structure (C) of native cationic cyclization antibody 4C6... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ruk | ||||||
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Title | Crystal structure (C) of native cationic cyclization antibody 4C6 fab at pH 4.6 with a data set collected at SSRL beamline 9-1 | ||||||
![]() | (immunoglobulin igg2a, ...) x 2 | ||||||
![]() | IMMUNE SYSTEM / immunoglobulin / catalytic antibody / water oxidation / amino acid modification | ||||||
Function / homology | ![]() 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 / phagocytosis, engulfment / endosome to lysosome transport ...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 / phagocytosis, engulfment / endosome to lysosome transport / positive regulation of endocytosis / antigen processing and presentation / immunoglobulin mediated immune response / positive regulation of phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / multivesicular body / complement activation, classical pathway / antigen binding / response to bacterium / positive regulation of immune response / antibacterial humoral response / blood microparticle / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhu, X. / Wentworth Jr., P. / Wentworth, A.D. / Eschenmoser, A. / Lerner, R.A. / Wilson, I.A. | ||||||
![]() | ![]() Title: Probing the antibody-catalyzed water-oxidation pathway at atomic resolution. Authors: Zhu, X. / Wentworth Jr., P. / Wentworth, A.D. / Eschenmoser, A. / Lerner, R.A. / Wilson, I.A. #1: ![]() 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 no suitable sequence data base reference was available at the time of processing this file. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202.8 KB | Display | ![]() |
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PDB format | ![]() | 160.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.8 KB | Display | ![]() |
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Full document | ![]() | 474.9 KB | Display | |
Data in XML | ![]() | 22.8 KB | Display | |
Data in CIF | ![]() | 34.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ru9C ![]() 1ruaC ![]() 1rulC ![]() 1rumC ![]() 1rupC ![]() 1ruqC ![]() 1rurC ![]() 1ncwS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
-Antibody , 2 types, 2 molecules LH
#1: Antibody | Mass: 24219.010 Da / Num. of mol.: 1 / Fragment: fab / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Antibody | Mass: 23816.590 Da / Num. of mol.: 1 / Fragment: fab / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 4 types, 435 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/BEZ.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BEZ.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-ACT / | ||
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#4: Chemical | ChemComp-BEZ / | ||
#5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.85 Å3/Da / Density % sol: 56.4 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1M sodium acetate, 0.2 M ammonium acetate, 15% (w/v) PEG 4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 295 K / pH: 5.5 / 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: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 28, 2001 / Details: flat mirror |
Radiation | Monochromator: Single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9706 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 111974 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rsym value: 0.044 / Net I/σ(I): 38.7 |
Reflection shell | Resolution: 1.4→1.42 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.7 / % possible all: 99.4 |
Reflection | *PLUS Rmerge(I) obs: 0.044 |
Reflection shell | *PLUS % possible obs: 99.4 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1NCW Resolution: 1.4→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→50 Å
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Refine LS restraints |
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Software | *PLUS Name: shelxl / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.21 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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