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- PDB-1a4j: DIELS ALDER CATALYTIC ANTIBODY GERMLINE PRECURSOR -

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Basic information

Entry
Database: PDB / ID: 1a4j
TitleDIELS ALDER CATALYTIC ANTIBODY GERMLINE PRECURSOR
Components
  • IMMUNOGLOBULIN, DIELS ALDER CATALYTIC ANTIBODY (HEAVY CHAIN)Antibody
  • IMMUNOGLOBULIN, DIELS ALDER CATALYTIC ANTIBODY (LIGHT CHAIN)Antibody
KeywordsIMMUNOGLOBULIN / ANTIBODY / CATALYTIC ANTIBODY / DIELS ALDER / GERMLINE
Function / homology
Function and homology information


IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / IgG immunoglobulin complex / immunoglobulin mediated immune response ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / IgG immunoglobulin complex / immunoglobulin mediated immune response / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / blood microparticle / Potential therapeutics for SARS / adaptive immune response / immune response / extracellular space / extracellular exosome / extracellular region / 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 / 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
Immunoglobulin kappa constant
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSpiller, B.W. / Romesburg, F.E. / Schultz, P.G. / Stevens, R.C.
CitationJournal: Science / Year: 1998
Title: Immunological origins of binding and catalysis in a Diels-Alderase antibody.
Authors: Romesberg, F.E. / Spiller, B. / Schultz, P.G. / Stevens, R.C.
History
DepositionJan 30, 1998Processing site: BNL
Revision 1.0May 13, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IMMUNOGLOBULIN, DIELS ALDER CATALYTIC ANTIBODY (LIGHT CHAIN)
H: IMMUNOGLOBULIN, DIELS ALDER CATALYTIC ANTIBODY (HEAVY CHAIN)
A: IMMUNOGLOBULIN, DIELS ALDER CATALYTIC ANTIBODY (LIGHT CHAIN)
B: IMMUNOGLOBULIN, DIELS ALDER CATALYTIC ANTIBODY (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)94,6004
Polymers94,6004
Non-polymers00
Water4,756264
1
L: IMMUNOGLOBULIN, DIELS ALDER CATALYTIC ANTIBODY (LIGHT CHAIN)
H: IMMUNOGLOBULIN, DIELS ALDER CATALYTIC ANTIBODY (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)47,3002
Polymers47,3002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-20 kcal/mol
Surface area20290 Å2
MethodPISA
2
A: IMMUNOGLOBULIN, DIELS ALDER CATALYTIC ANTIBODY (LIGHT CHAIN)
B: IMMUNOGLOBULIN, DIELS ALDER CATALYTIC ANTIBODY (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)47,3002
Polymers47,3002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-20 kcal/mol
Surface area20460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.900, 49.330, 145.000
Angle α, β, γ (deg.)90.00, 108.74, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody IMMUNOGLOBULIN, DIELS ALDER CATALYTIC ANTIBODY (LIGHT CHAIN) / Antibody


Mass: 23706.475 Da / Num. of mol.: 2 / Fragment: FAB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell line: 25F2 / Plasmid: P4XH / Production host: Escherichia coli (E. coli) / Strain (production host): 25F2 / References: UniProt: P01834
#2: Antibody IMMUNOGLOBULIN, DIELS ALDER CATALYTIC ANTIBODY (HEAVY CHAIN) / Antibody


Mass: 23593.459 Da / Num. of mol.: 2 / Fragment: FAB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell line: 25F2 / Plasmid: P4XH / Production host: Escherichia coli (E. coli) / Strain (production host): 25F2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.84 Å3/Da / Density % sol: 51.3 %
Crystal growpH: 6
Details: 19% PEG 8K, 20% GLYCEROL, 200MM MG(CH3COO)2, 10MM CDS04 100MM BISTRIS PH 6.0
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
210 mMTris-HCl1drop
3100 mM1dropNaCl
41 mMmethionine1drop
519 %PEG1reservoir
620 %glycerol1reservoir
7200 mMmagnesium acetate1reservoir
8100 mMBis-Tris1reservoir
910 mM1reservoirCdSO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.87
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: WIGGLER
RadiationMonochromator: MONOCHROMATOR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 63217 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 33.7 Å2 / Rsym value: 0.044 / Net I/σ(I): 16
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.27 / % possible all: 95.4
Reflection
*PLUS
Rmerge(I) obs: 0.044
Reflection shell
*PLUS
% possible obs: 95.4 % / Rmerge(I) obs: 0.27

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A4K

1a4k


Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.292 4197 10 %RANDOM
Rwork0.229 ---
obs0.229 49380 98.5 %-
Displacement parametersBiso mean: 36.4 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6902 0 2 274 7178
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.383
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d30.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.749
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.1→2.2 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.355 473 10 %
Rwork0.245 4049 -
obs--95.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PR
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg30.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.749
LS refinement shell
*PLUS
Rfactor obs: 0.245

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