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- PDB-1rul: Crystal Structure (D) of u.v.-irradiated cationic cyclization ant... -

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Basic information

Entry
Database: PDB / ID: 1rul
TitleCrystal Structure (D) of u.v.-irradiated cationic cyclization antibody 4C6 Fab at pH 5.6 with a data set collected at SSRL beamline 11-1.
Components(immunoglobulin igg2a, ...) x 2
KeywordsIMMUNE SYSTEM / immunoglobulin / catalytic antibody / water oxidation / amino acid modification
Function / homology
Function and homology information


positive regulation of B cell activation / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / early endosome to late endosome transport / 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 / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / early endosome to late endosome transport / 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 / immunoglobulin complex, circulating / immunoglobulin receptor binding / antigen processing and presentation / positive regulation of endocytosis / immunoglobulin mediated immune response / complement activation, classical pathway / positive regulation of phagocytosis / antigen binding / multivesicular body / response to bacterium / positive regulation of immune response / antibacterial humoral response / plasma membrane
Similarity search - Function
: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins ...: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / BENZOIC ACID / Immunoglobulin heavy constant gamma 2A / :
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsZhu, 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
DepositionDec 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jun 5, 2013Group: Non-polymer description
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: immunoglobulin igg2a, light chain
H: immunoglobulin igg2a, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6178
Polymers48,0682
Non-polymers5506
Water6,143341
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint-25 kcal/mol
Surface area19860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.920, 63.920, 265.725
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody immunoglobulin igg2a, light chain


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
#2: Antibody immunoglobulin igg2a, heavy chain


Mass: 23832.590 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

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Non-polymers , 4 types, 347 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M tri-sodium citrate, 0.2M ammonium acetate, 15% (w/v) PEG 4000, pH 5.6, 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
IDConc.Common nameCrystal-IDSol-IDDetails
126 mg/mlFab1drop
20.1 Msodium acetate1droppH5.5
315 %(w/v)PEG40001reservoir
40.2 Mammonium acetate1reservoir
50.1 Mtrisodium citrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1.03317 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 10, 2002 / Details: flat mirror
RadiationMonochromator: Single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 42866 / % possible obs: 90.7 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rsym value: 0.08 / Net I/σ(I): 22.6
Reflection shellResolution: 1.88→1.92 Å / Mean I/σ(I) obs: 1.4 / Rsym value: 0.46 / % possible all: 72.4
Reflection
*PLUS
Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 72.4 %

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Processing

Software
NameClassification
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NCW

1ncw


Resolution: 1.88→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2424 -random
Rwork0.206 ---
all-40313 --
obs-40313 79.8 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refinement stepCycle: LAST / Resolution: 1.88→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3382 0 37 341 3760
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0275
X-RAY DIFFRACTIONs_zero_chiral_vol0.034
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.037
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.015
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.08
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg1.9
X-RAY DIFFRACTIONs_plane_restr0.028
X-RAY DIFFRACTIONs_chiral_restr0.034

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