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- PDB-1fj1: LYME DISEASE ANTIGEN OSPA IN COMPLEX WITH NEUTRALIZING ANTIBODY F... -

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Basic information

Entry
Database: PDB / ID: 1fj1
TitleLYME DISEASE ANTIGEN OSPA IN COMPLEX WITH NEUTRALIZING ANTIBODY FAB LA-2
Components
  • HYBRIDOMA ANTIBODY LA2 (HEAVY CHAIN)
  • HYBRIDOMA ANTIBODY LA2 (LIGHT CHAIN)
  • OUTER SURFACE PROTEIN A
KeywordsIMMUNE SYSTEM / OSPA / LYME DISEASE / ANTIBODY FAB FRAGMENT / NEUTRALIZING EPITOPE
Function / homology
Function and homology information


Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / phagocytosis, engulfment / immunoglobulin complex, circulating / immunoglobulin receptor binding / immunoglobulin mediated immune response / complement activation, classical pathway / positive regulation of phagocytosis / antigen binding / B cell differentiation / cell outer membrane / positive regulation of immune response / antibacterial humoral response / cell surface / extracellular space / extracellular region / membrane / plasma membrane
Similarity search - Function
C1 set domains (antibody constant domain-like) / Outer Surface Protein A; domain 3 - #1 / Outer surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / Outer Surface Protein A; domain 3 / : / Lipocalin / : / Prokaryotic membrane lipoprotein lipid attachment site profile. ...C1 set domains (antibody constant domain-like) / Outer Surface Protein A; domain 3 - #1 / Outer surface lipoprotein, Borrelia / Outer surface lipoprotein domain superfamily / Borrelia lipoprotein / Outer Surface Protein A; domain 3 / : / Lipocalin / : / Prokaryotic membrane lipoprotein lipid attachment site profile. / 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 / Alpha-Beta Complex / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Immunoglobulin kappa constant / Immunoglobulin heavy constant gamma 2B / Outer surface protein A / Outer surface protein A
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsDing, W. / Lawson, C.L.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Structural identification of a key protective B-cell epitope in Lyme disease antigen OspA.
Authors: Ding, W. / Huang, X. / Yang, X. / Dunn, J.J. / Luft, B.J. / Koide, S. / Lawson, C.L.
History
DepositionAug 7, 2000Deposition site: RCSB / Processing site: RCSB
SupersessionOct 11, 2000ID: 2OSP
Revision 1.0Oct 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYBRIDOMA ANTIBODY LA2 (LIGHT CHAIN)
B: HYBRIDOMA ANTIBODY LA2 (HEAVY CHAIN)
C: HYBRIDOMA ANTIBODY LA2 (LIGHT CHAIN)
D: HYBRIDOMA ANTIBODY LA2 (HEAVY CHAIN)
E: OUTER SURFACE PROTEIN A
F: OUTER SURFACE PROTEIN A


Theoretical massNumber of molelcules
Total (without water)147,8396
Polymers147,8396
Non-polymers00
Water4,648258
1
A: HYBRIDOMA ANTIBODY LA2 (LIGHT CHAIN)
B: HYBRIDOMA ANTIBODY LA2 (HEAVY CHAIN)
F: OUTER SURFACE PROTEIN A


Theoretical massNumber of molelcules
Total (without water)73,9203
Polymers73,9203
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-28 kcal/mol
Surface area31630 Å2
MethodPISA
2
C: HYBRIDOMA ANTIBODY LA2 (LIGHT CHAIN)
D: HYBRIDOMA ANTIBODY LA2 (HEAVY CHAIN)
E: OUTER SURFACE PROTEIN A


Theoretical massNumber of molelcules
Total (without water)73,9203
Polymers73,9203
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.079, 129.462, 143.738
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is an Fab/antigen complex composed of chains A, B, and F, or alternately C, D, and E

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Components

#1: Antibody HYBRIDOMA ANTIBODY LA2 (LIGHT CHAIN) / LA2 FAB


Mass: 23608.090 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source
Details: LA-2 HYBRIDOMA, GIFT OF M.M. SIMON, MAX PLANCK INSTUTUT, FREIBURG
Source: (natural) Mus musculus (house mouse) / References: UniProt: P01837*PLUS
#2: Antibody HYBRIDOMA ANTIBODY LA2 (HEAVY CHAIN) / LA2 FAB


Mass: 22629.268 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Details: LA-2 HYBRIDOMA / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01867*PLUS
#3: Protein OUTER SURFACE PROTEIN A / OSPA


Mass: 27682.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Strain: B31 / Plasmid: PET9C / Production host: Escherichia coli (E. coli) / References: UniProt: P14013, UniProt: P0CL66*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 3.15 Å3/Da / Density % sol: 60.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.15
Details: 100 mM sodium cacodylate, 100 mM sodium acetate, 10 % (w/v) PEG 3350, pH 6.15, VAPOR DIFFUSION, HANGING DROP, temperature 4K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
2100 mMsodium cacodylate1reservoir
3100 mMsodium acetate1reservoir
410 %(w/v)PEG33501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: BRANDEIS / Detector: CCD / Date: May 1, 1997 / Details: COLLIMATOR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.68→20 Å / Num. all: 51741 / Num. obs: 221681 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 50.4 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 19.9
Reflection shellResolution: 2.68→2.78 Å / Redundancy: 4 % / Rmerge(I) obs: 0.112 / Num. unique all: 5136 / % possible all: 98.4
Reflection
*PLUS
Num. obs: 51741 / Num. measured all: 221681
Reflection shell
*PLUS
% possible obs: 98.4 % / Num. unique obs: 5136 / Num. measured obs: 20967

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GAF, PDB ENTRY 1OSP

1gaf

1osp


Resolution: 2.68→19.83 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1428286.9 / Data cutoff high rms absF: 1428286.9 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.281 5165 10.1 %RANDOM, 10%
Rwork0.226 ---
all-51197 --
obs-51197 96.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.6764 Å2 / ksol: 0.318791 e/Å3
Displacement parametersBiso mean: 52.8 Å2
Baniso -1Baniso -2Baniso -3
1--3.16 Å20 Å20 Å2
2---5.25 Å20 Å2
3---8.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.68→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10284 0 0 258 10542
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d0.94
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 2.68→2.85 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.347 822 9.9 %
Rwork0.275 7449 -
obs--94.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94

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