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Yorodumi- PDB-1rum: Crystal structure (F) of H2O2-soaked cationic cyclization antibod... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rum | ||||||
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Title | Crystal structure (F) of H2O2-soaked cationic cyclization antibody 4C6 fab at pH 8.5 with a data set collected at SSRL beamline 9-1. | ||||||
Components |
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Keywords | IMMUNE SYSTEM / immunoglobulin / catalytic antibody / water oxidation / amino acid modification | ||||||
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: 1.48 Å | ||||||
Authors | Zhu, X. / Wentworth Jr., P. / Wentworth, A.D. / Eschenmoser, A. / Lerner, R.A. / Wilson, I.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 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: 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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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rum.cif.gz | 214.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rum.ent.gz | 169.3 KB | Display | PDB format |
PDBx/mmJSON format | 1rum.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1rum_validation.pdf.gz | 460.2 KB | Display | wwPDB validaton report |
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Full document | 1rum_full_validation.pdf.gz | 465.7 KB | Display | |
Data in XML | 1rum_validation.xml.gz | 25.7 KB | Display | |
Data in CIF | 1rum_validation.cif.gz | 39.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ru/1rum ftp://data.pdbj.org/pub/pdb/validation_reports/ru/1rum | HTTPS FTP |
-Related structure data
Related structure data | 1ru9C 1ruaC 1rukC 1rulC 1rupC 1ruqC 1rurC 1ncwS 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: 24235.010 Da / Num. of mol.: 1 / Fragment: fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: 129G1X+ / References: UniProt: Q8K0F8, UniProt: Q58EU8*PLUS | ||
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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) Mus musculus (house mouse) / Strain: 129G1X+ / References: UniProt: P01865 | ||
#3: Chemical | ChemComp-BEZ / | ||
#4: Chemical | #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: 2.87 Å3/Da / Density % sol: 56.9 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M tris hydrochloride, pH 8.5, 0.2 M sodium acetate, 15% (w/v) PEG 4000, 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: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.9706 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 20, 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: 1.48→50 Å / Num. all: 91933 / Num. obs: 91933 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.07 / Net I/σ(I): 29.6 |
Reflection shell | Resolution: 1.48→1.52 Å / Mean I/σ(I) obs: 1.4 / Rsym value: 0.534 / % possible all: 98.8 |
Reflection | *PLUS Num. obs: 92687 / Rmerge(I) obs: 0.07 |
Reflection shell | *PLUS % possible obs: 98.8 % / Mean I/σ(I) obs: 1.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NCW Resolution: 1.48→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: 1.48→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 % | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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