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- PDB-1d5b: UNLIGANDED MATURE OXY-COPE CATALYTIC ANTIBODY -

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Basic information

Entry
Database: PDB / ID: 1d5b
TitleUNLIGANDED MATURE OXY-COPE CATALYTIC ANTIBODY
Components
  • chimeric OXY-COPE catalytic ANTIBODY AZ-28 (HEAVY chain)
  • chimeric OXY-COPE catalytic ANTIBODY AZ-28 (light chain)
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / immunoglobulin complex / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / Fc-gamma receptor I complex binding / CD22 mediated BCR regulation / complement-dependent cytotoxicity / immunoglobulin complex / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / complement activation, classical pathway / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / antigen binding / 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 / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / Potential therapeutics for SARS / blood microparticle / 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 C1-set / Immunoglobulin C1-set domain ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / IgM heavy chain variable region / Immunoglobulin kappa constant / Immunoglobulin heavy constant gamma 1 / Immunoglobulin gamma-1 heavy chain / Anti-colorectal carcinoma light chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsMundorff, E.C. / Hanson, M.A. / Schultz, P.G. / Stevens, R.C.
CitationJournal: Biochemistry / Year: 2000
Title: Conformational effects in biological catalysis: an antibody-catalyzed oxy-cope rearrangement.
Authors: Mundorff, E.C. / Hanson, M.A. / Varvak, A. / Ulrich, H. / Schultz, P.G. / Stevens, R.C.
History
DepositionOct 6, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_fragment / _struct_ref_seq.db_align_beg ..._entity.pdbx_fragment / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.ref_id / _struct_ref_seq.seq_align_beg

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: chimeric OXY-COPE catalytic ANTIBODY AZ-28 (light chain)
B: chimeric OXY-COPE catalytic ANTIBODY AZ-28 (HEAVY chain)
L: chimeric OXY-COPE catalytic ANTIBODY AZ-28 (light chain)
H: chimeric OXY-COPE catalytic ANTIBODY AZ-28 (HEAVY chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4885
Polymers94,3754
Non-polymers1121
Water1,33374
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
L: chimeric OXY-COPE catalytic ANTIBODY AZ-28 (light chain)
H: chimeric OXY-COPE catalytic ANTIBODY AZ-28 (HEAVY chain)


Theoretical massNumber of molelcules
Total (without water)47,1882
Polymers47,1882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-29 kcal/mol
Surface area19040 Å2
MethodPISA, PQS
3
A: chimeric OXY-COPE catalytic ANTIBODY AZ-28 (light chain)
B: chimeric OXY-COPE catalytic ANTIBODY AZ-28 (HEAVY chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3003
Polymers47,1882
Non-polymers1121
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-24 kcal/mol
Surface area18850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)77.420, 80.670, 134.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody chimeric OXY-COPE catalytic ANTIBODY AZ-28 (light chain)


Mass: 23563.236 Da / Num. of mol.: 2
Fragment: chimeric fab fragment (UNP Q7TS98 reisues 23-129, P01834 residues 1-104)
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN WAS PRODUCED AS A CHIMERIC FAB FRAGMENT. THE VARIABLE DOMAINS (CHAINS A,L 1-107, CHAINS B,H 1-113) ARE MURINE. THE CONSTANT DOMAINS (CHAINS A,L 108-211 AND CHAINS B,H 113-214) ARE HUMAN.
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Genus: Mus, Homo / Species: , / Plasmid: PAZ-28 / Gene: IGKC / Production host: Escherichia coli (E. coli) / References: UniProt: Q7TS98, UniProt: P01834
#2: Antibody chimeric OXY-COPE catalytic ANTIBODY AZ-28 (HEAVY chain)


Mass: 23624.328 Da / Num. of mol.: 2
Fragment: chimeric fab fragment (UNP K7T9I5 residues 1-112, P0DOX5 residues 120-220)
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN WAS PRODUCED AS A CHIMERIC FAB FRAGMENT. THE VARIABLE DOMAINS (CHAINS A,L 1-107, CHAINS B,H 1-113) ARE MURINE. THE CONSTANT DOMAINS (CHAINS A,L 108-211 AND CHAINS B,H 113-214) ARE HUMAN.
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Genus: Mus, Homo / Species: , / Plasmid: PAZ-28 / Production host: Escherichia coli (E. coli)
References: UniProt: K7T9I5, UniProt: P0DOX5, UniProt: P01857*PLUS
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Compound detailsAntibody AZ-28 catalyzes the oxy-Cope rearrangement.

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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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 25%PEG 1000, 100mM sodium acetate, 300mM CdCl2, 100mM ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
2100 mM1dropNaCl
310 mMTris-HCl1drop
41 mMmethionine1drop
525 %PEG10001reservoir
6100 mMsodium acetate1reservoir
7300 mMcadmium chloride1reservoir
8100 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 4, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 18775 / Num. obs: 103369 / % possible obs: 86.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.28 / Num. unique all: 531 / % possible all: 70.5
Reflection
*PLUS
Num. obs: 19606 / % possible obs: 91.2 % / Num. measured all: 103369
Reflection shell
*PLUS
% possible obs: 70.5 % / Mean I/σ(I) obs: 4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.4refinement
RefinementResolution: 2.8→20 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 452246.71 / Data cutoff high rms absF: 452246.71 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1674 9.9 %RANDOM
Rwork0.232 ---
all0.241 18775 --
obs0.232 16916 79.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.81 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso mean: 51 Å2
Baniso -1Baniso -2Baniso -3
1-16.06 Å20 Å20 Å2
2---10.97 Å20 Å2
3----5.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.34 Å
Luzzati d res low-7 Å
Luzzati sigma a0.4 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6642 0 1 74 6717
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d0.99
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.384 183 10.5 %
Rwork0.289 1567 -
obs--50.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CIS_PEPTIDE.PARAMTOP.LIB
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4PAR.LIB
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.231
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.99

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