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- PDB-1rur: Crystal Structure (I) of native Diels-Alder antibody 13G5 Fab at ... -

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Basic information

Entry
Database: PDB / ID: 1rur
TitleCrystal Structure (I) of native Diels-Alder antibody 13G5 Fab at pH 8.0 with a data set collected at SSRL beamline 9-1.
Components
  • immunoglobulin 13G5, heavy chain
  • immunoglobulin 13G5, light chain
KeywordsIMMUNE SYSTEM / immunoglobulin / catalytic antibody / water oxidation / amino acid modification
Function / homology
Function and homology information


Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / phagocytosis, engulfment / immunoglobulin mediated immune response / complement activation, classical pathway / immunoglobulin complex / antigen binding / B cell differentiation / positive regulation of phagocytosis / positive regulation of immune response / antibacterial humoral response / adaptive immune response / defense response to bacterium / external side of plasma membrane / extracellular space / extracellular region / metal ion binding / plasma membrane / cytoplasm
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 C1-set ...: / 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
Immunoglobulin kappa constant / Ig gamma-1 chain C region, membrane-bound form / Igh protein / :
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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: Science / Year: 1998
Title: An antibody exo diels-alderase inhibitor complex at 1.95 angstrom resolution
Authors: Heine, A. / Stura, E.A. / Yli-kauhaluoma, J.T. / Gao, C. / Deng, Q. / Beno, B.R. / 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: Version format compliance
Revision 1.3Jul 24, 2019Group: Advisory / Data collection / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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_atom_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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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

Downloads & links

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Assembly

Deposited unit
L: immunoglobulin 13G5, light chain
H: immunoglobulin 13G5, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1384
Polymers47,0072
Non-polymers1312
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-88 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.275, 40.310, 67.631
Angle α, β, γ (deg.)90.00, 109.91, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody immunoglobulin 13G5, light chain


Mass: 23806.480 Da / Num. of mol.: 1 / Fragment: fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: 13G5 murine hybridima / References: UniProt: Q5XKG4, UniProt: P01837*PLUS
#2: Antibody immunoglobulin 13G5, heavy chain


Mass: 23200.771 Da / Num. of mol.: 1 / Fragment: fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: 13G5 murine hybridima / References: UniProt: P01869, UniProt: Q569W9*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M imidazole, pH 8.0, 0.2 M zinc acetate, 5-7% (v/v) isopropanol, 20% (w/v) PEG 3000, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 295 K / pH: 7.4 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlFab1droppH7.4
220 %(w/v)PEG30001reservoir
30.2 Mzinc acetate1reservoir
45-7 %(v/v)isopropyl alcohol1reservoir
50.1 Mimidazole1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.99184 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 7, 2002 / Details: flat mirror
RadiationMonochromator: single crystal si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99184 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 71213 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / Rsym value: 0.047 / Net I/σ(I): 24
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 1.6 / Rsym value: 0.536 / % possible all: 97.9
Reflection
*PLUS
Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 97.9 %

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Processing

Software
NameClassification
SHELXL-97refinement
HKL-2000data reduction
CNSrefinement
HKL-2000data collection
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A3L

1a3l


Resolution: 1.5→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 4021 -random
Rwork0.191 ---
all-65588 --
obs-65588 84 %-
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 2 372 3682
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.024
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.026
X-RAY DIFFRACTIONs_zero_chiral_vol0.036
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.046
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.012
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.051
X-RAY DIFFRACTIONs_approx_iso_adps0.066
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.256
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2
X-RAY DIFFRACTIONs_plane_restr0.026
X-RAY DIFFRACTIONs_chiral_restr0.036

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