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- PDB-1fn4: CRYSTAL STRUCTURE OF FAB198, AN EFFICIENT PROTECTOR OF ACETYLCHOL... -

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Basic information

Entry
Database: PDB / ID: 1fn4
TitleCRYSTAL STRUCTURE OF FAB198, AN EFFICIENT PROTECTOR OF ACETYLCHOLINE RECEPTOR AGAINST MYASTHENOGENIC ANTIBODIES
Components(MONOCLONAL ANTIBODY AGAINST ACETYLCHOLINE RECEPTOR) x 2
KeywordsIMMUNE SYSTEM / FAB198
Function / homology
Function and homology information


immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral 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 / 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
Ig kappa chain C region, B allele / Ig gamma-2A chain C region
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsPoulas, K. / Eliopoulos, E. / Vatzaki, E. / Navaza, J. / Kontou, M.
CitationJournal: Eur.J.Biochem. / Year: 2001
Title: Crystal structure of Fab198, an efficient protector of the acetylcholine receptor against myasthenogenic antibodies.
Authors: Poulas, K. / Eliopoulos, E. / Vatzaki, E. / Navaza, J. / Kontou, M. / Oikonomakos, N. / Acharya, K.R. / Tzartos, S.J.
History
DepositionAug 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MONOCLONAL ANTIBODY AGAINST ACETYLCHOLINE RECEPTOR
B: MONOCLONAL ANTIBODY AGAINST ACETYLCHOLINE RECEPTOR
C: MONOCLONAL ANTIBODY AGAINST ACETYLCHOLINE RECEPTOR
D: MONOCLONAL ANTIBODY AGAINST ACETYLCHOLINE RECEPTOR


Theoretical massNumber of molelcules
Total (without water)93,6634
Polymers93,6634
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: MONOCLONAL ANTIBODY AGAINST ACETYLCHOLINE RECEPTOR
D: MONOCLONAL ANTIBODY AGAINST ACETYLCHOLINE RECEPTOR


Theoretical massNumber of molelcules
Total (without water)46,8312
Polymers46,8312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-25 kcal/mol
Surface area18950 Å2
MethodPISA, PQS
3
A: MONOCLONAL ANTIBODY AGAINST ACETYLCHOLINE RECEPTOR
B: MONOCLONAL ANTIBODY AGAINST ACETYLCHOLINE RECEPTOR


Theoretical massNumber of molelcules
Total (without water)46,8312
Polymers46,8312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-23 kcal/mol
Surface area19200 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)169.780, 169.780, 182.570
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein MONOCLONAL ANTIBODY AGAINST ACETYLCHOLINE RECEPTOR


Mass: 23177.717 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P01835*PLUS
#2: Protein MONOCLONAL ANTIBODY AGAINST ACETYLCHOLINE RECEPTOR


Mass: 23653.658 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P20760*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 3.51 Å3/Da / Density % sol: 47.5 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.5
Details: 12 MG/ML FAB198, 1.6 M AS, 0.4 M CACL2, 0.1 M PB, 0.1% PEG 10000, PH 7.5, VAPOR DIFFUSION, SITTING DROP
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop / pH: 8.1
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
112 mg/mlprotein1drop
21.6 Mammonium sulfate1reservoir
30.4 M1reservoirCaCl2
40.1 Mphosphate1reservoirpH8.1
50.1 %PEG100001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 32382 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.046
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.217 / % possible all: 98.9
Reflection
*PLUS
Num. measured all: 112032
Reflection shell
*PLUS
% possible obs: 98.9 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.1refinement
RefinementResolution: 2.8→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
Details: ANOMALOUS PEPTIDE BOND DISTANCES CORRESPOND TO REGIONS POORLY DEFINED BY ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.294 -5 %RANDOM
Rwork0.198 ---
obs0.198 32382 98 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.32 Å
Luzzati d res low-20 Å
Luzzati sigma a0.5 Å-
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6578 0 0 136 6714
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.8→2.93 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2337 --
Rwork0.3018 2896 -
obs--71.5 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / Num. reflection Rfree: 1619 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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