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- PDB-25c8: CATALYTIC ANTIBODY 5C8, FAB-HAPTEN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 25c8
TitleCATALYTIC ANTIBODY 5C8, FAB-HAPTEN COMPLEX
Components(IGG 5C8) x 2
KeywordsCATALYTIC ANTIBODY / FAB / RING CLOSURE REACTION
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 / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / 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 / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin mediated immune response / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / 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 / Immunoglobulins / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-GEP / 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: 2 Å
AuthorsGruber, K. / Wilson, I.A.
Citation
Journal: Biochemistry / Year: 1999
Title: Structural basis for antibody catalysis of a disfavored ring closure reaction.
Authors: Gruber, K. / Zhou, B. / Houk, K.N. / Lerner, R.A. / Shevlin, C.G. / Wilson, I.A.
#1: Journal: To be Published
Title: Ligand-Induced Conformational Changes in a Catalytic Antibody: Comparison of the Bound and Unbound Structure of Fab 5C8
Authors: Gruber, K. / Heine, A. / Stura, E.A. / Shevlin, C.G. / Wilson, I.A.
History
DepositionMar 18, 1998Processing site: BNL
Revision 1.0Mar 23, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGG 5C8
H: IGG 5C8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5803
Polymers46,2462
Non-polymers3331
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-17 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.000, 80.000, 64.900
Angle α, β, γ (deg.)90.00, 118.00, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-213-

HOH

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Components

#1: Antibody IGG 5C8


Mass: 23148.482 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01837
#2: Antibody IGG 5C8


Mass: 23097.658 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01869
#3: Chemical ChemComp-GEP / N-METHYL-N-(PARA-GLUTARAMIDOPHENYL-ETHYL)-PIPERIDINIUM ION


Mass: 333.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H29N2O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growpH: 5.5 / Details: pH 5.5
Crystal grow
*PLUS
Temperature: 22.5 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116 mg/mlprotein1drop
20.1 Msodium acetate1drop
314 %PEG100001reservoir
40.2 MTris-malate1reservoir

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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 MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 33080 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 29.2 Å2 / Rsym value: 0.057 / Net I/σ(I): 16.9
Reflection shellResolution: 2→2.03 Å / Mean I/σ(I) obs: 2.9 / Rsym value: 0.304 / % possible all: 93.4
Reflection
*PLUS
Num. measured all: 231822 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 93.4 % / Rmerge(I) obs: 0.304

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FREE FAB 5C8

Resolution: 2→25 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.292 2505 7.6 %RANDOM
Rwork0.229 ---
obs0.229 33080 96.7 %-
Displacement parametersBiso mean: 39.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.72 Å20 Å25.84 Å2
2--7.7 Å20 Å2
3---10.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3251 0 24 232 3507
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d30
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.7
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.531.5
X-RAY DIFFRACTIONx_mcangle_it4.052
X-RAY DIFFRACTIONx_scbond_it3.292
X-RAY DIFFRACTIONx_scangle_it4.692.5
LS refinement shellResolution: 2→2.03 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 117 7.9 %
Rwork0.35 1473 -
obs--93.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2NME.PARTOPH19.SOL
X-RAY DIFFRACTION3NME.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.229 / Rfactor obs: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg30
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.7
LS refinement shell
*PLUS
Rfactor Rwork: 0.35

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