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- PDB-1a3l: CATALYSIS OF A DISFAVORED REACTION: AN ANTIBODY EXO DIELS-ALDERAS... -

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Basic information

Entry
Database: PDB / ID: 1a3l
TitleCATALYSIS OF A DISFAVORED REACTION: AN ANTIBODY EXO DIELS-ALDERASE-TSA-INHIBITOR COMPLEX AT 1.95 A RESOLUTION
Components
  • IMMUNOGLOBULIN FAB 13G5 (HEAVY CHAIN)
  • IMMUNOGLOBULIN FAB 13G5 (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN / DIELS-ALDER / DISFAVORED REACTION / CATALYTIC ANTIBODY
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 / antigen binding / positive regulation of phagocytosis / B cell differentiation / positive regulation of immune response / antibacterial humoral response / defense response to bacterium / external side of plasma membrane / extracellular space / extracellular region / plasma membrane / cytoplasm
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
1-CARBOXY-1'-[(DIMETHYLAMINO)-CARBONYL]FERROCENE / : / : / Immunoglobulin kappa constant / Ig gamma-1 chain C region, membrane-bound form
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHeine, A. / Wilson, I.A.
CitationJournal: 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
DepositionJan 22, 1998Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IMMUNOGLOBULIN FAB 13G5 (LIGHT CHAIN)
H: IMMUNOGLOBULIN FAB 13G5 (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3083
Polymers47,0072
Non-polymers3011
Water5,567309
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-21 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.900, 40.500, 67.700
Angle α, β, γ (deg.)90.00, 109.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody IMMUNOGLOBULIN FAB 13G5 (LIGHT CHAIN)


Mass: 23806.480 Da / Num. of mol.: 1 / Fragment: IMMUNOGLOBULIN FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: 13G5 MURINE HYBRIDOMA / References: GenBank: 1911624, UniProt: P01837*PLUS
#2: Antibody IMMUNOGLOBULIN FAB 13G5 (HEAVY CHAIN)


Mass: 23200.771 Da / Num. of mol.: 1 / Fragment: IMMUNOGLOBULIN FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: 13G5 MURINE HYBRIDOMA / References: EMBL: Y08011, UniProt: P01869*PLUS
#3: Chemical ChemComp-CFC / 1-CARBOXY-1'-[(DIMETHYLAMINO)-CARBONYL]FERROCENE


Mass: 301.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15FeNO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.4 Å3/Da / Density % sol: 52 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 %mPEG20001reservoir
20.1 Mcacodylate1reservoir

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Data collection

DiffractionMean temperature: 97 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1996 / Details: PT COATED FUSED SILICA X-RAY MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. obs: 32813 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rsym value: 0.039 / Net I/σ(I): 30.5
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 10 / Rsym value: 0.127 / % possible all: 84
Reflection
*PLUS
Num. measured all: 188444 / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 84 % / Rmerge(I) obs: 0.127

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-96model building
SHELXL-96refinement
SHELXL-96phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BBJ

1bbj


Resolution: 1.95→10 Å / Num. parameters: 14607 / Num. restraintsaints: 14033 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST. 28 (1995) 53-56 THERE WAS NO CLEAR DENSITY FOR AN EXTERNAL LOOP REGION IN THE CONSTANT HEAVY CHAIN (H 129 - H 135).
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1628 5 %EVERY 20TH REFLECTION
all0.1881 32572 --
obs0.184 -90 %-
Solvent computationSolvent model: MOEWS&KRETSINGER,J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 3173 / Occupancy sum non hydrogen: 3614
Refinement stepCycle: LAST / Resolution: 1.95→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3319 0 19 309 3647
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_similar_dist0.001
X-RAY DIFFRACTIONs_from_restr_planes0.34
X-RAY DIFFRACTIONs_zero_chiral_vol0.094
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.089
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.072
X-RAY DIFFRACTIONs_approx_iso_adps0

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