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- PDB-1axs: MATURE OXY-COPE CATALYTIC ANTIBODY WITH HAPTEN -

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Basic information

Entry
Database: PDB / ID: 1axs
TitleMATURE OXY-COPE CATALYTIC ANTIBODY WITH HAPTEN
Components(OXY-COPE CATALYTIC ANTIBODY) x 2
KeywordsCATALYTIC ANTIBODY / OXY-COPE / FAB FRAGMENT
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
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 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
: / Chem-HOP / : / Immunoglobulin heavy constant gamma 1 / Ig-like domain-containing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMundorff, E.C. / Ulrich, H.D. / Stevens, R.C.
CitationJournal: Nature / Year: 1997
Title: The interplay between binding energy and catalysis in the evolution of a catalytic antibody.
Authors: Ulrich, H.D. / Mundorff, E. / Santarsiero, B.D. / Driggers, E.M. / Stevens, R.C. / Schultz, P.G.
History
DepositionOct 20, 1997Processing site: BNL
Revision 1.0Feb 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_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

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Assembly

Deposited unit
L: OXY-COPE CATALYTIC ANTIBODY
H: OXY-COPE CATALYTIC ANTIBODY
A: OXY-COPE CATALYTIC ANTIBODY
B: OXY-COPE CATALYTIC ANTIBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,94114
Polymers94,2794
Non-polymers1,66210
Water3,333185
1
L: OXY-COPE CATALYTIC ANTIBODY
H: OXY-COPE CATALYTIC ANTIBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0838
Polymers47,1402
Non-polymers9446
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-48 kcal/mol
Surface area19930 Å2
MethodPISA
2
A: OXY-COPE CATALYTIC ANTIBODY
B: OXY-COPE CATALYTIC ANTIBODY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8586
Polymers47,1402
Non-polymers7194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-35 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.780, 81.500, 128.200
Angle α, β, γ (deg.)90.00, 93.43, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(0.768442, -0.001566, 0.639918), (-0.014427, -0.999785, 0.014878), (0.639757, -0.020665, -0.768299)-91.5869, 76.2005, 141.3224
2given(0.768696, -0.044396, 0.638071), (-0.03005, -0.998993, -0.033307), (0.638908, 0.006428, -0.769256)-88.578, 82.7215, 139.7903
3given(0.753593, -0.005915, 0.657315), (-0.015668, -0.999837, 0.008965), (0.657155, -0.017055, -0.753563)-92.9298, 77.0969, 138.763
4given(0.757525, -0.058684, 0.650163), (-0.060283, -0.997984, -0.019841), (0.650017, -0.024163, -0.759536)-19.1128, 80.2548, 165.847
5given(0.763982, -0.061151, 0.642334), (-0.048339, -0.998126, -0.037528), (0.643425, -0.002379, -0.765506)-87.9134, 83.8807, 139.8223

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Components

#1: Antibody OXY-COPE CATALYTIC ANTIBODY


Mass: 23529.176 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT
Source method: isolated from a genetically manipulated source
Details: CHIMERIC FAB FRAGMENT / Source: (gene. exp.) Homo sapiens (human) / Strain: SWISS WEBSTER
Description: THE PROTEIN WAS PRODUCED AS CHIMERIC FAB FRAGMENT. THE CONSTANT DOMAINS ARE HUMAN, THE VARIABLE DOMAINS ARE MURINE. PRODUCTION BY EXPRESSION FROM PHOA PROMOTER
Cell: B LYMPHOCYTE / Cell line: AZ-28 HYBRIDOMA / Fragment: CHAIN L, A, 108 - 211, CHAIN H, B, 114 - 214 / Organ: SPLEEN / Plasmid: PAZ-28 / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): 25F2 / References: GenBank: 243868, UniProt: Q7Z3Y4*PLUS
#2: Antibody OXY-COPE CATALYTIC ANTIBODY


Mass: 23610.342 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT
Source method: isolated from a genetically manipulated source
Details: CHIMERIC FAB FRAGMENT / Source: (gene. exp.) Homo sapiens (human) / Strain: SWISS WEBSTER
Description: THE PROTEIN WAS PRODUCED AS CHIMERIC FAB FRAGMENT. THE CONSTANT DOMAINS ARE HUMAN, THE VARIABLE DOMAINS ARE MURINE. PRODUCTION BY EXPRESSION FROM PHOA PROMOTER
Cell: B LYMPHOCYTE / Cell line: AZ-28 HYBRIDOMA / Fragment: CHAIN L, A, 108 - 211, CHAIN H, B, 114 - 214 / Organ: SPLEEN / Plasmid: PAZ-28 / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): 25F2 / References: UniProt: P01857
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-HOP / (1S,2S,5S)2-(4-GLUTARIDYLBENZYL)-5-PHENYL-1-CYCLOHEXANOL / OXY-COPE-HAPTEN


Mass: 381.465 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H27NO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.3 Å3/Da / Density % sol: 40 %
Crystal growpH: 4.6
Details: PROTEIN WAS CRYSTALLIZED FROM 25%PEG 1000, 0.1 M SODIUM ACETATE, PH 4.6, 0.3 M CDCL2 AND 0.1 M AMMONIUM SULFATE IN THE PRESENCE OF 2MM HAPTEN.
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125 %PEG10001drop
20.1 Msodium acetate1drop
30.3 M1dropCdCl2
40.1 Mammonium sulfate1drop
52 mMhapten 11drop

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Data collection

DiffractionMean temperature: 94 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1997 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 24768 / % possible obs: 90.9 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 16
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.142 / Mean I/σ(I) obs: 6 / Rsym value: 0.142 / % possible all: 87.5

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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 6FAB

6fab


Resolution: 2.6→20 Å / Rfactor Rfree error: 0.0062 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.0001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.305 2434 10 %RANDOM
Rwork0.2 ---
obs0.2 24768 91.1 %-
Displacement parametersBiso mean: 36.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6638 0 63 186 6887
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d30.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.65
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.51.5
X-RAY DIFFRACTIONx_mcangle_it5.52
X-RAY DIFFRACTIONx_scbond_it5.32
X-RAY DIFFRACTIONx_scangle_it7.12.5
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Weight Biso : 2 / Weight position: 300

Ens-IDDom-IDNCS model detailsRms dev Biso (Å2)Rms dev position (Å)
11RESTRAINED11.20.06
229.290.14
336.190.06
443.880.04
LS refinement shellResolution: 2.6→2.72 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.384 294 10 %
Rwork0.293 2695 -
obs--87.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2CPH.PARCISP.TOP
X-RAY DIFFRACTION3CISP.PARAMCPH.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg30.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.65

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