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- PDB-1aqk: THREE-DIMENSIONAL STRUCTURE OF A HUMAN FAB WITH HIGH AFFINITY FOR... -

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Basic information

Entry
Database: PDB / ID: 1aqk
TitleTHREE-DIMENSIONAL STRUCTURE OF A HUMAN FAB WITH HIGH AFFINITY FOR TETANUS TOXOID
Components(FAB B7-15A2) x 2
KeywordsIMMUNOGLOBULIN / HUMAN FAB / ANTI-TETANUS TOXOID / HIGH AFFINITY / CRYSTAL PACKING MOTIF / PROGRAMMING PROPENSITY TO CRYSTALLIZE
Function / homology
Function and homology information


IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / complement-dependent cytotoxicity / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / complement-dependent cytotoxicity / Fc epsilon receptor (FCERI) signaling / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin mediated immune response / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / complement activation, classical pathway / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / 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 / blood microparticle / Potential therapeutics for SARS / adaptive immune response / immune response / extracellular space / extracellular exosome / 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 / Immunoglobulins / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin lambda constant 1 / Immunoglobulin heavy constant gamma 1 / Immunoglobulin lambda constant 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsFaber, C. / Fan, Z. / Edmundson, A.B.
CitationJournal: Immunotechnology / Year: 1998
Title: Three-dimensional structure of a human Fab with high affinity for tetanus toxoid.
Authors: Faber, C. / Shan, L. / Fan, Z. / Guddat, L.W. / Furebring, C. / Ohlin, M. / Borrebaeck, C.A. / Edmundson, A.B.
History
DepositionJul 30, 1997Processing site: BNL
Revision 1.0Feb 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Polymer sequence
Category: entity_poly / pdbx_database_status ...entity_poly / pdbx_database_status / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.1Aug 2, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: FAB B7-15A2
H: FAB B7-15A2


Theoretical massNumber of molelcules
Total (without water)46,9892
Polymers46,9892
Non-polymers00
Water5,206289
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-32 kcal/mol
Surface area19930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.700, 78.600, 74.600
Angle α, β, γ (deg.)90.00, 104.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody FAB B7-15A2


Mass: 22699.068 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Details: IMMUNOGLOBULIN HUMAN FAB / Source: (natural) Homo sapiens (human) / References: UniProt: P01842, UniProt: P0DOY3*PLUS
#2: Antibody FAB B7-15A2


Mass: 24290.426 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source / Details: IMMUNOGLOBULIN HUMAN FAB / Source: (natural) Homo sapiens (human) / References: UniProt: P01857
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.46 Å3/Da / Density % sol: 49.98 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Method: unknown / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
193 mg/mlFab11
231 mMTris11
37.3 %(w/v)PEG800011
40.8 mM11NaN3

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Data collection

DiffractionMean temperature: 286 K
Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: May 1, 1992 / Details: MIRRORS
RadiationMonochromator: NO / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.84→20 Å / Num. obs: 32194 / % possible obs: 81 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 33.1
Reflection shellResolution: 1.84→1.96 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 8.5 / % possible all: 49
Reflection
*PLUS
Num. all: 39263

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Processing

Software
NameVersionClassification
XENGENdata collection
XENGENdata reduction
X-PLORmodel building
TNT5Erefinement
X-PLORrefinement
XENGENdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FB4

2fb4


Resolution: 1.84→20 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.185 --
obs-32494 81 %
Solvent computationSolvent model: BABINET SCALING / Bsol: 150 Å2 / ksol: 0.7 e/Å3
Refinement stepCycle: LAST / Resolution: 1.84→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3308 0 0 289 3597
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01734020.8
X-RAY DIFFRACTIONt_angle_deg2.7946161.6
X-RAY DIFFRACTIONt_dihedral_angle_d27.119770
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.01662
X-RAY DIFFRACTIONt_gen_planes0.0165025
X-RAY DIFFRACTIONt_it4.933926
X-RAY DIFFRACTIONt_nbd0.04213110
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg27.10
X-RAY DIFFRACTIONt_planar_d0.012
X-RAY DIFFRACTIONt_plane_restr0.0165

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