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- PDB-1ncw: Cationic Cyclization Antibody 4C6 in Complex with Benzoic Acid -

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Basic information

Entry
Database: PDB / ID: 1ncw
TitleCationic Cyclization Antibody 4C6 in Complex with Benzoic Acid
Components(IMMUNOGLOBULIN IGG2A) x 2
KeywordsIMMUNE SYSTEM / immunoglobulin / catalytic antibody / cationic cyclization reaction
Function / homology
Function and homology information


positive regulation of B cell activation / phagocytosis, recognition / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / endosome to lysosome transport ...positive regulation of B cell activation / phagocytosis, recognition / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / endosome to lysosome transport / antigen processing and presentation / immunoglobulin mediated immune response / regulation of proteolysis / positive regulation of endocytosis / immunoglobulin complex / complement activation, classical pathway / antigen binding / multivesicular body / positive regulation of phagocytosis / response to bacterium / positive regulation of immune response / adaptive immune response / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
BENZOIC ACID / Immunoglobulin heavy constant gamma 2A / Igk protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsZhu, X. / Wilson, I.A.
CitationJournal: 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 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2003Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IMMUNOGLOBULIN IGG2A
H: IMMUNOGLOBULIN IGG2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5267
Polymers48,0362
Non-polymers4905
Water10,395577
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-23 kcal/mol
Surface area19950 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.072, 64.072, 265.646
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11H-914-

HOH

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Components

#1: Antibody IMMUNOGLOBULIN IGG2A


Mass: 24219.010 Da / Num. of mol.: 1 / Fragment: Antibody FAB fragment 4C6, light chain / Source method: isolated from a natural source / Details: PURIFIED FROM ASCITIC FLUID / Source: (natural) Mus musculus (house mouse) / Strain: 129G1X+ / References: UniProt: Q58EU8*PLUS
#2: Antibody IMMUNOGLOBULIN IGG2A


Mass: 23816.590 Da / Num. of mol.: 1 / Fragment: Antibody FAB fragment 4C6, 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*PLUS
#3: Chemical ChemComp-BEZ / BENZOIC ACID


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


Mass: 18.015 Da / Num. of mol.: 577 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAN APPROPRIATE SEQUENCE DATABASE REFERENCE WAS NOT AVAILABLE AT THE TIME OF PROCESSING.

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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: 56.66 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 5.6
Details: PEG4000, ammonium acetate, tri-sodium citrate, pH 5.6, Evaporation, temperature 295K
Crystal grow
*PLUS
pH: 5.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
126 mg/mlprotein1drop
20.1 Msodium acetate1droppH5.5
315-18 %(w/v)PEG40001reservoir
40.2 Mammonium acetate1reservoir
50.1 Mtri-sodium citrate dihydrate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 3, 2000
RadiationMonochromator: Double cyrstal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 137097 / Num. obs: 117957 / % possible obs: 86 % / Observed criterion σ(F): 0 / Redundancy: 3.85 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 26.4
Reflection shellResolution: 1.3→1.32 Å / Rmerge(I) obs: 0.688 / Mean I/σ(I) obs: 1.5 / % possible all: 69.6
Reflection
*PLUS
Lowest resolution: 50 Å / Redundancy: 3.9 %
Reflection shell
*PLUS
% possible obs: 69.6 % / Num. unique obs: 4684

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Processing

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

1mrd


Resolution: 1.3→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Initial refinement begun with CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.208 6915 -RANDOM
Rwork0.158 ---
all-117843 --
obs-117843 86 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 0
Refinement stepCycle: LAST / Resolution: 1.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3380 0 33 577 3990
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.027
X-RAY DIFFRACTIONs_approx_iso_adps0.083
X-RAY DIFFRACTIONs_from_restr_planes0.0325
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_zero_chiral_vol0.067
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.081
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.051
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / Num. reflection Rfree: 7132 / % 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_deg2.3

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