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- PDB-1axt: IMMUNE VERSUS NATURAL SELECTION: ANTIBODY ALDOLASES WITH THE RATE... -

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Basic information

Entry
Database: PDB / ID: 1axt
TitleIMMUNE VERSUS NATURAL SELECTION: ANTIBODY ALDOLASES WITH THE RATES OF NATURAL ENZYMES
Components(IMMUNOGLOBULIN IGG2A) x 2
KeywordsIMMUNOGLOBULIN / ANTIBODY FAB' / CATALYST / ALDOLASE REACTION
Function / homology
Function and homology information


positive regulation of B cell activation / phagocytosis, recognition / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / endosome to lysosome transport ...positive regulation of B cell activation / phagocytosis, recognition / early endosome to late endosome transport / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / endosome to lysosome transport / antigen processing and presentation / immunoglobulin mediated immune response / regulation of proteolysis / positive regulation of endocytosis / complement activation, classical pathway / antigen binding / multivesicular body / positive regulation of phagocytosis / response to bacterium / positive regulation of immune response / 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
: / Immunoglobulin heavy constant gamma 2A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsHeine, A. / Wilson, I.A.
CitationJournal: Science / Year: 1997
Title: Immune versus natural selection: antibody aldolases with enzymic rates but broader scope.
Authors: Barbas 3rd., C.F. / Heine, A. / Zhong, G. / Hoffmann, T. / Gramatikova, S. / Bjornestedt, R. / List, B. / Anderson, J. / Stura, E.A. / Wilson, I.A. / Lerner, R.A.
History
DepositionOct 20, 1997Processing site: BNL
Revision 1.0Oct 28, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 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

Downloads & links

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Assembly

Deposited unit
L: IMMUNOGLOBULIN IGG2A
H: IMMUNOGLOBULIN IGG2A


Theoretical massNumber of molelcules
Total (without water)47,6262
Polymers47,6262
Non-polymers00
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-26 kcal/mol
Surface area19760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.500, 65.300, 132.600
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 IMMUNOGLOBULIN IGG2A


Mass: 23796.426 Da / Num. of mol.: 1 / Fragment: FAB' FRAGMENT 33F12 / Source method: isolated from a natural source / Details: MONOCLONAL ANTIBODY IGG2A FAB' FRAGMENT / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C / References: PIR: S16112
#2: Antibody IMMUNOGLOBULIN IGG2A


Mass: 23829.885 Da / Num. of mol.: 1 / Fragment: FAB' FRAGMENT 33F12 / Source method: isolated from a natural source / Details: MONOCLONAL ANTIBODY IGG2A FAB' FRAGMENT / Source: (natural) Mus musculus (house mouse) / Strain: BALB/C / References: UniProt: P01865
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.45 Å3/Da / Density % sol: 50 %
Crystal growpH: 7.4
Details: PROTEIN WAS CRYSTALLIZED FROM 18% PEG 4000, 10% ISOPROPANOL, 100 MM HEPES, PH 7.4.
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118 %PEG400011
20.1 MHEPES11
310 %isopropanol11

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Data collection

DiffractionMean temperature: 97 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1996 / Details: PT COATED FUSED SILICA X-RAY MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.15→40 Å / Num. obs: 26432 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 10 % / Rsym value: 0.065 / Net I/σ(I): 25
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 5.6 / Rsym value: 0.302 / % possible all: 95
Reflection
*PLUS
Num. measured all: 264288 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 95 % / Rmerge(I) obs: 0.302

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
MERLOTphasing
SHELXL-96refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CGR

2cgr


Resolution: 2.15→10 Å / Num. parameters: 14365 / Num. restraintsaints: 14062 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: THE INITIAL REFINEMENT WAS BEGUN USING X-PLOR. RESIDUES H 128 TO H136 ARE IN WEAK OR NO ELECTRON DENSITY. THEY WERE REFINED WITH ZERO OCCUPANCY AND THE LISTED COORDINATES ARE THEREFORE NOT RELIABLE.
RfactorNum. reflection% reflectionSelection details
Rfree0.3167 1304 5 %EVERY 20TH REFLECTION
all0.2144 26080 --
obs0.2108 -96.1 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 3233 / Occupancy sum non hydrogen: 3556
Refinement stepCycle: LAST / Resolution: 2.15→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3350 0 0 248 3598
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.021
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.324
X-RAY DIFFRACTIONs_zero_chiral_vol0.088
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.082
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.015
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.068
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-96 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg30
X-RAY DIFFRACTIONs_improper_angle_d
X-RAY DIFFRACTIONs_improper_angle_deg1.7

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