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- PDB-1ru9: Crystal Structure (A) of u.v.-irradiated cationic cyclization ant... -

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Basic information

Entry
Database: PDB / ID: 1ru9
TitleCrystal Structure (A) of u.v.-irradiated cationic cyclization antibody 4C6 Fab at pH 4.6 with a data set collected in-house.
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 / 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 / humoral immune response mediated by circulating immunoglobulin / early endosome to late endosome transport / 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 / positive regulation of endocytosis / immunoglobulin mediated immune response / regulation of proteolysis / complement activation, classical pathway / antigen binding / positive regulation of phagocytosis / multivesicular body / response to bacterium / positive regulation of immune 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 / Immunoglobulin-like fold ...: / 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 / Immunoglobulin-like fold / Immunoglobulins / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.4Aug 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.pdbx_leaving_atom_flag / _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
Remark 999sequence no suitable sequence data base reference was available at the time of processing this file.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)48,7099
Polymers48,0682
Non-polymers6427
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-26 kcal/mol
Surface area19910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.073, 64.073, 266.041
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, 249 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#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.: 242 / 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: 2.85 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M sodium acetate, pH 4.6, 0.2 M ammonium 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
IDConc.Common nameCrystal-IDSol-IDDetails
115 %(w/v)PEG40001reservoir
20.2 Mammonium acetate1reservoir
30.1 Msodium acetate1reservoirpH4.6
426 mg/mlFab1drop
50.1 Msodium acetate1droppH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 28, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 18691 / % possible obs: 92 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.091 / Net I/σ(I): 12.3
Reflection shellResolution: 2.5→2.54 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.447 / % possible all: 90
Reflection
*PLUS
Rmerge(I) obs: 0.091
Reflection shell
*PLUS
% possible obs: 90.9 %

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Processing

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

1ncw


Resolution: 2.5→50 Å / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1037 -random
Rwork0.192 ---
obs-17609 87.1 %-
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3382 0 43 242 3667
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d27.5
X-RAY DIFFRACTIONc_improper_angle_d0.86
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86

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