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- PDB-1nd0: CATIONIC CYCLIZATION ANTIBODY 4C6 COMPLEX WITH TRANSITION STATE ANALOG -

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Basic information

Entry
Database: PDB / ID: 1nd0
TitleCATIONIC CYCLIZATION ANTIBODY 4C6 COMPLEX WITH TRANSITION STATE ANALOG
Components(IMMUNOGLOBULIN IGG2A) x 2
KeywordsIMMUNE SYSTEM / Immunoglobulin / catalytic antibody / cationic cyclization reaction
Function / homology
Function and homology information


positive regulation of B cell activation / humoral immune response mediated by circulating immunoglobulin / early endosome to late endosome transport / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment / endosome to lysosome transport ...positive regulation of B cell activation / humoral immune response mediated by circulating immunoglobulin / early endosome to late endosome transport / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / regulation of proteolysis / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / phagocytosis, engulfment / endosome to lysosome transport / positive regulation of endocytosis / antigen processing and presentation / immunoglobulin mediated immune response / positive regulation of phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / multivesicular body / complement activation, classical pathway / antigen binding / response to bacterium / positive regulation of immune response / antibacterial humoral response / blood microparticle / immune response / extracellular space / extracellular exosome / metal ion binding / 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
Chem-DP4 / Ig gamma-2A chain C region, membrane-bound form / Igk protein / :
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsZhu, X. / Wilson, I.A.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Structural Basis for Antibody Catalysis of a Cationic Cyclization Reaction
Authors: Zhu, X. / Heine, A. / Monnat, F. / Houk, K.N. / Janda, K.D. / Wilson, I.A.
History
DepositionDec 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE AN APPROPRIATE SEQUENCE DATABASE REFERENCE WAS NOT AVAILABLE AT THE TIME OF PROCESSING.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMMUNOGLOBULIN IGG2A
B: IMMUNOGLOBULIN IGG2A
C: IMMUNOGLOBULIN IGG2A
D: IMMUNOGLOBULIN IGG2A
E: IMMUNOGLOBULIN IGG2A
F: IMMUNOGLOBULIN IGG2A
G: IMMUNOGLOBULIN IGG2A
H: IMMUNOGLOBULIN IGG2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,52416
Polymers192,1428
Non-polymers1,3828
Water7,098394
1
A: IMMUNOGLOBULIN IGG2A
B: IMMUNOGLOBULIN IGG2A
hetero molecules

C: IMMUNOGLOBULIN IGG2A
D: IMMUNOGLOBULIN IGG2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7628
Polymers96,0714
Non-polymers6914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area10980 Å2
ΔGint-76 kcal/mol
Surface area37960 Å2
MethodPISA
2
E: IMMUNOGLOBULIN IGG2A
F: IMMUNOGLOBULIN IGG2A
hetero molecules

G: IMMUNOGLOBULIN IGG2A
H: IMMUNOGLOBULIN IGG2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,7628
Polymers96,0714
Non-polymers6914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area11130 Å2
ΔGint-74 kcal/mol
Surface area37790 Å2
MethodPISA
3
A: IMMUNOGLOBULIN IGG2A
B: IMMUNOGLOBULIN IGG2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3814
Polymers48,0362
Non-polymers3452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
C: IMMUNOGLOBULIN IGG2A
D: IMMUNOGLOBULIN IGG2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3814
Polymers48,0362
Non-polymers3452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: IMMUNOGLOBULIN IGG2A
F: IMMUNOGLOBULIN IGG2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3814
Polymers48,0362
Non-polymers3452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
G: IMMUNOGLOBULIN IGG2A
H: IMMUNOGLOBULIN IGG2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3814
Polymers48,0362
Non-polymers3452
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)36.572, 95.164, 141.058
Angle α, β, γ (deg.)75.51, 88.64, 89.28
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody
IMMUNOGLOBULIN IGG2A


Mass: 24219.010 Da / Num. of mol.: 4 / Fragment: IMMUNOGLOBULIN FAB FRAGMENT, light chain / Source method: isolated from a natural source / Details: Purified from Ascitic fluid / Source: (natural) Mus musculus (house mouse) / Strain: 129G1X+ / References: UniProt: Q8K0F8, UniProt: Q58EU8*PLUS
#2: Antibody
IMMUNOGLOBULIN IGG2A


Mass: 23816.590 Da / Num. of mol.: 4 / Fragment: IMMUNOGLOBULIN FAB FRAGMENT, heavy chain / Source method: isolated from a natural source / Details: Purified from Ascitic fluid / Source: (natural) Mus musculus (house mouse) / Strain: 129G1X+ / References: UniProt: P01865
#3: Chemical
ChemComp-DP4 / (1s,4s)-4-[dimethyl(phenyl)silyl]-1-methylpiperidine 1-oxide


Mass: 249.424 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H23NOSi
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.42 Å3/Da / Density % sol: 48.86 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 5.5
Details: ammonium sulfate, dioxane, tri-sodium citrate dihydrate, pH 5.5, evaporation, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
126 mg/mlprotein1drop
20.1 Msodium acetate1droppH5.5
31.7 Mammonium sulfate1reservoir
410 %(v/v)dioxane1reservoir
50.1 Mtri-sodium citrate dihydrate1reservoirpH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 4, 2001
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 67638 / Num. obs: 53415 / % possible obs: 79.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 30.9 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 8.7
Reflection shellResolution: 2.45→2.49 Å / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 1.5 / % possible all: 78.4
Reflection
*PLUS
Lowest resolution: 50 Å / Redundancy: 1.7 %
Reflection shell
*PLUS
% possible obs: 78.4 % / Redundancy: 1.7 % / Num. unique obs: 2598 / Mean I/σ(I) obs: 1.5

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Processing

Software
NameClassification
HKL-2000data collection
HKL-2000data reduction
AMoREphasing
CNSrefinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NCW

1ncw


Resolution: 2.45→50 Å / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.286 2539 5 %RANDOM
Rwork0.242 ---
all-53415 --
obs-49304 72.9 %-
Displacement parametersBiso mean: 35 Å2
Refinement stepCycle: LAST / Resolution: 2.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13520 0 88 394 14002
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d27
X-RAY DIFFRACTIONc_improper_angle_d0.088
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.09

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