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- PDB-1fsk: COMPLEX FORMATION BETWEEN A FAB FRAGMENT OF A MONOCLONAL IGG ANTI... -

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Basic information

Entry
Database: PDB / ID: 1fsk
TitleCOMPLEX FORMATION BETWEEN A FAB FRAGMENT OF A MONOCLONAL IGG ANTIBODY AND THE MAJOR ALLERGEN FROM BIRCH POLLEN BET V 1
Components
  • ANTIBODY HEAVY CHAIN FAB
  • IMMUNOGLOBULIN KAPPA LIGHT CHAIN
  • MAJOR POLLEN ALLERGEN BET V 1-A
KeywordsIMMUNE SYSTEM / Bet v 1 / Bv16 Fab fragment / antibody allergen complex
Function / homology
Function and homology information


abscisic acid binding / abscisic acid-activated signaling pathway / protein phosphatase inhibitor activity / B cell differentiation / defense response / signaling receptor activity / extracellular region / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Pathogenesis-related protein Bet v I family / Pathogenesis-related proteins Bet v I family signature. / Bet v I type allergen / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / : / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / : ...Pathogenesis-related protein Bet v I family / Pathogenesis-related proteins Bet v I family signature. / Bet v I type allergen / Bet v I/Major latex protein / Pathogenesis-related protein Bet v 1 family / : / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / : / 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 / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Immunoglobulin kappa constant / Major pollen allergen Bet v 1-A
Similarity search - Component
Biological speciesBetula pendula (European white birch)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsMirza, O. / Henriksen, A. / Ipsen, H. / Larsen, J. / Wissenbach, M. / Spangfort, M. / Gajhede, M.
CitationJournal: J.Immunol. / Year: 2000
Title: Dominant epitopes and allergic cross-reactivity: complex formation between a Fab fragment of a monoclonal murine IgG antibody and the major allergen from birch pollen Bet v 1.
Authors: Mirza, O. / Henriksen, A. / Ipsen, H. / Larsen, J.N. / Wissenbach, M. / Spangfort, M.D. / Gajhede, M.
History
DepositionSep 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MAJOR POLLEN ALLERGEN BET V 1-A
B: IMMUNOGLOBULIN KAPPA LIGHT CHAIN
C: ANTIBODY HEAVY CHAIN FAB
D: MAJOR POLLEN ALLERGEN BET V 1-A
E: IMMUNOGLOBULIN KAPPA LIGHT CHAIN
F: ANTIBODY HEAVY CHAIN FAB
G: MAJOR POLLEN ALLERGEN BET V 1-A
H: IMMUNOGLOBULIN KAPPA LIGHT CHAIN
I: ANTIBODY HEAVY CHAIN FAB
J: MAJOR POLLEN ALLERGEN BET V 1-A
K: IMMUNOGLOBULIN KAPPA LIGHT CHAIN
L: ANTIBODY HEAVY CHAIN FAB


Theoretical massNumber of molelcules
Total (without water)259,97712
Polymers259,97712
Non-polymers00
Water00
1
A: MAJOR POLLEN ALLERGEN BET V 1-A
B: IMMUNOGLOBULIN KAPPA LIGHT CHAIN
C: ANTIBODY HEAVY CHAIN FAB


Theoretical massNumber of molelcules
Total (without water)64,9943
Polymers64,9943
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: MAJOR POLLEN ALLERGEN BET V 1-A
E: IMMUNOGLOBULIN KAPPA LIGHT CHAIN
F: ANTIBODY HEAVY CHAIN FAB


Theoretical massNumber of molelcules
Total (without water)64,9943
Polymers64,9943
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: MAJOR POLLEN ALLERGEN BET V 1-A
H: IMMUNOGLOBULIN KAPPA LIGHT CHAIN
I: ANTIBODY HEAVY CHAIN FAB


Theoretical massNumber of molelcules
Total (without water)64,9943
Polymers64,9943
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: MAJOR POLLEN ALLERGEN BET V 1-A
K: IMMUNOGLOBULIN KAPPA LIGHT CHAIN
L: ANTIBODY HEAVY CHAIN FAB


Theoretical massNumber of molelcules
Total (without water)64,9943
Polymers64,9943
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.653, 99.145, 108.905
Angle α, β, γ (deg.)105.70, 98.32, 97.62
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

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Components

#1: Protein
MAJOR POLLEN ALLERGEN BET V 1-A / BET V I-A / BETVI ALLERGEN


Mass: 17427.576 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Betula pendula (European white birch) / Production host: Escherichia coli (E. coli) / References: UniProt: P15494
#2: Antibody
IMMUNOGLOBULIN KAPPA LIGHT CHAIN / BV16 FAB-FRAGMENT / KAPPA MOPC21 CODING SEQUENCE


Mass: 23730.113 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: BALB/C MICE / Production host: Escherichia coli (E. coli) / References: UniProt: P01837
#3: Antibody
ANTIBODY HEAVY CHAIN FAB / HEAVY CHAIN OF THE MONOCLONAL ANTIBODY MST2


Mass: 23836.660 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: BALB/C MICE / Production host: Escherichia coli (E. coli)
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: 3.56 Å3/Da / Density % sol: 65.49 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 12% peg 6000, 0.1M sodium citrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlprotein1drop
212 %PEG60001drop
30.1 Msodium citrate1drop
40.01 %sodium azide1drop
512 %PEG60001reservoir
60.01 %sodium azide1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 21, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / % possible obs: 95.5 % / Biso Wilson estimate: 49.2 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 19.85
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 0.37 / Num. unique all: 6763 / % possible all: 83.8
Reflection
*PLUS
Num. obs: 80241 / Num. measured all: 181008
Reflection shell
*PLUS
% possible obs: 83.8 % / Num. unique obs: 6763 / Num. measured obs: 11123

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.5refinement
RefinementResolution: 2.9→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 551538.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 3726 5.1 %RANDOM
Rwork0.253 ---
obs0.253 73464 92.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.46 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso mean: 63.3 Å2
Baniso -1Baniso -2Baniso -3
1-11.2 Å25.26 Å21.18 Å2
2---4.64 Å2-8.71 Å2
3----6.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.46 Å
Luzzati d res low-20 Å
Luzzati sigma a0.66 Å0.58 Å
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18308 0 0 0 18308
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it2.751.5
X-RAY DIFFRACTIONc_mcangle_it4.662
X-RAY DIFFRACTIONc_scbond_it3.772
X-RAY DIFFRACTIONc_scangle_it5.82.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.419 519 4.9 %
Rwork0.39 10014 -
obs--79.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2CIS_PEPT
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94

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