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- PDB-1cf8: Convergence of catalytic antibody and terpene cyclase mechanisms:... -

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Basic information

Entry
Database: PDB / ID: 1cf8
TitleConvergence of catalytic antibody and terpene cyclase mechanisms: polyene cyclization directed by carbocation-pi interactions
Components
  • PROTEIN (CATALYTIC ANTIBODY 19A4 (HEAVY CHAIN))
  • PROTEIN (CATALYTIC ANTIBODY 19A4 (LIGHT CHAIN))
KeywordsCATALYTIC ANTIBODY / TERPENOID SYNTHASE / CARBOCATION / CYCLIZATION CASCADE
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 / 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 / extracellular space / 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 / 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
: / Chem-HAZ / Immunoglobulin kappa constant / Immunoglobulin heavy constant gamma 2B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPaschall, C.M. / Hasserodt, J. / Jones, T. / Lerner, R.A. / Janda, K.D. / Christianson, D.W.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 1999
Title: Convergence of Catalytic Antibody and Terpene Cyclase Mechanisms: Polyene Cyclization Directed by Carbocation-pi Interactions
Authors: Paschall, C.M. / Hasserodt, J. / Jones, T. / Lerner, R.A. / Janda, K.D. / Christianson, D.W.
History
DepositionMar 24, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 28, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: 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 / pdbx_struct_conn_angle / 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.ptnr1_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 999 SEQUENCE The proper sequence database reference not availabe due to fragments of variable region

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: PROTEIN (CATALYTIC ANTIBODY 19A4 (LIGHT CHAIN))
H: PROTEIN (CATALYTIC ANTIBODY 19A4 (HEAVY CHAIN))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6695
Polymers46,9852
Non-polymers6843
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-39 kcal/mol
Surface area19600 Å2
MethodPISA
2
L: PROTEIN (CATALYTIC ANTIBODY 19A4 (LIGHT CHAIN))
H: PROTEIN (CATALYTIC ANTIBODY 19A4 (HEAVY CHAIN))
hetero molecules

L: PROTEIN (CATALYTIC ANTIBODY 19A4 (LIGHT CHAIN))
H: PROTEIN (CATALYTIC ANTIBODY 19A4 (HEAVY CHAIN))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,33910
Polymers93,9704
Non-polymers1,3696
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)101.300, 70.300, 69.600
Angle α, β, γ (deg.)90.00, 114.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody PROTEIN (CATALYTIC ANTIBODY 19A4 (LIGHT CHAIN))


Mass: 23484.854 Da / Num. of mol.: 1 / Fragment: FAB, VARIABLE REGION / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: 129G1X+(MOUSE)/P3X63AG8.653 (MYELOMA) / Strain: 129G1X+/BOY / References: UniProt: P01837*PLUS
#2: Antibody PROTEIN (CATALYTIC ANTIBODY 19A4 (HEAVY CHAIN))


Mass: 23500.123 Da / Num. of mol.: 1 / Fragment: FAB, VARIABLE REGION / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: 129G1X+(MOUSE)/P3X63AG8.653 (MYELOMA) / Strain: 129G1X+/BOY / References: UniProt: P01867*PLUS
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-HAZ / 4-{4-[2-(1A,7A-DIMETHYL-4-OXY-OCTAHYDRO-1-OXA-4-AZA-CYCLOPROPA[A]NAPHTHALEN-4-YL) -ACETYLAMINO]-PHENYLCARBAMOYL}-BUTYRIC ACID


Mass: 459.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H33N3O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS PROTEIN IS A FAB FRAGMENT PRODUCED UPON THE DIGESTION OF FULL-LENGTH MURINE MONOCLONAL ...THIS PROTEIN IS A FAB FRAGMENT PRODUCED UPON THE DIGESTION OF FULL-LENGTH MURINE MONOCLONAL ANTIBODY BY PAPAIN.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 47.8 %
Description: USED MODEL OF SEQUENCE WITH ONLY VARYING RESIDUES CHANGED TO ALANINE.
Crystal growpH: 7
Details: DROP: 11.4 MG/ML FAB, 10MM CDCL2, 50 MM TRIS, PH 7.0, RESERVOIR: 30% PEG 6000, 100 MM HEPES PH 7.9, pH 7.00
Crystal
*PLUS
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
111.4 mg/mlFab1drop
210 mM1dropCdCl2
310 mMcomplex1drop
450 mMTris1drop
530 %PEG60001reservoir
6100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 17, 1998 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 11531 / % possible obs: 93.5 % / Observed criterion σ(I): 2 / Redundancy: 3.24 % / Biso Wilson estimate: 39.1 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 19.31
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 6.7 / % possible all: 80.2
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å / % possible obs: 93.5 % / Observed criterion σ(I): 2 / Redundancy: 3.24 % / Biso Wilson estimate: 39.1 Å2
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 6.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YEF

1yef


Resolution: 2.7→20 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.257 597 5 %RANDOM
Rwork0.165 ---
obs-10933 93.5 %-
Displacement parametersBiso mean: 25.6 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3302 0 35 11 3348
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.47
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: 2.7→2.82 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.299 73 5 %
Rwork0.232 1039 -
obs--80.62 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARHAP.PROTOPHAP.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 20 Å / Rfactor obs: 0.165
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 25.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.47
LS refinement shell
*PLUS
Rfactor Rfree: 0.299 / Rfactor Rwork: 0.232

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