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- PDB-1c5d: THE CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF A RAT MONOCLONAL ANT... -

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Basic information

Entry
Database: PDB / ID: 1c5d
TitleTHE CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF A RAT MONOCLONAL ANTIBODY AGAINST THE MAIN IMMUNOGENIC REGION OF THE HUMAN MUSCLE ACETYLCHOLINE RECEPTOR
Components(MONOCLONAL ANTIBODY AGAINST THE MAIN IMMUNOGENIC REGION OF THE HUMAN MUSCLE ACETYLCHOLINE RECEPTOR) x 2
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN
Function / homology
Function and homology information


immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / extracellular exosome
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-2B chain C region
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKontou, M. / Leonidas, D.D. / Vatzaki, E.H. / Tsantili, P. / Mamalaki, A. / Oikonomakos, N.G. / Acharya, K.R. / Tzartos, S.J.
CitationJournal: Eur.J.Biochem. / Year: 2000
Title: The crystal structure of the Fab fragment of a rat monoclonal antibody against the main immunogenic region of the human muscle acetylcholine receptor.
Authors: Kontou, M. / Leonidas, D.D. / Vatzaki, E.H. / Tsantili, P. / Mamalaki, A. / Oikonomakos, N.G. / Acharya, K.R. / Tzartos, S.J.
History
DepositionNov 17, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Assembly

Deposited unit
L: MONOCLONAL ANTIBODY AGAINST THE MAIN IMMUNOGENIC REGION OF THE HUMAN MUSCLE ACETYLCHOLINE RECEPTOR
H: MONOCLONAL ANTIBODY AGAINST THE MAIN IMMUNOGENIC REGION OF THE HUMAN MUSCLE ACETYLCHOLINE RECEPTOR
A: MONOCLONAL ANTIBODY AGAINST THE MAIN IMMUNOGENIC REGION OF THE HUMAN MUSCLE ACETYLCHOLINE RECEPTOR
B: MONOCLONAL ANTIBODY AGAINST THE MAIN IMMUNOGENIC REGION OF THE HUMAN MUSCLE ACETYLCHOLINE RECEPTOR


Theoretical massNumber of molelcules
Total (without water)92,8304
Polymers92,8304
Non-polymers00
Water3,765209
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: MONOCLONAL ANTIBODY AGAINST THE MAIN IMMUNOGENIC REGION OF THE HUMAN MUSCLE ACETYLCHOLINE RECEPTOR
B: MONOCLONAL ANTIBODY AGAINST THE MAIN IMMUNOGENIC REGION OF THE HUMAN MUSCLE ACETYLCHOLINE RECEPTOR


Theoretical massNumber of molelcules
Total (without water)46,4152
Polymers46,4152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-26 kcal/mol
Surface area18320 Å2
MethodPISA, PQS
3
L: MONOCLONAL ANTIBODY AGAINST THE MAIN IMMUNOGENIC REGION OF THE HUMAN MUSCLE ACETYLCHOLINE RECEPTOR
H: MONOCLONAL ANTIBODY AGAINST THE MAIN IMMUNOGENIC REGION OF THE HUMAN MUSCLE ACETYLCHOLINE RECEPTOR


Theoretical massNumber of molelcules
Total (without water)46,4152
Polymers46,4152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-22 kcal/mol
Surface area18840 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)79.710, 110.080, 199.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein MONOCLONAL ANTIBODY AGAINST THE MAIN IMMUNOGENIC REGION OF THE HUMAN MUSCLE ACETYLCHOLINE RECEPTOR


Mass: 23361.033 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT, HEAVY CHAIN / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P01835*PLUS
#2: Protein MONOCLONAL ANTIBODY AGAINST THE MAIN IMMUNOGENIC REGION OF THE HUMAN MUSCLE ACETYLCHOLINE RECEPTOR


Mass: 23053.787 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT, LIGHT CHAIN / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P20761*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PROTEIN WAS SEQUENCED BY P.TSANTILI,S.J.TZARTOS, A.MAMALAKI, 1999, HIGH AFFINITY SINGLE-CHAIN ...THE PROTEIN WAS SEQUENCED BY P.TSANTILI,S.J.TZARTOS, A.MAMALAKI, 1999, HIGH AFFINITY SINGLE-CHAIN FV ANTIBODY FRAGMENTS PROTECTING THE HUMAN NICOTINIC ACETYLCHOLINE RECEPTOR. J. NEUROIMMUNOL. 94, 15-27. EMBL NUCLEOTIDE SEQUENCE DATABASE ACCESSION# AJ250888, RATTUS NORVEGICUS PARTIAL MRNA FOR IMMUNOGLOBULIN HEAVY CHAIN VARIABLE REGION, (IGLV GENE), MAB192 ACCESSION# AJ250889, RATTUS NORVEGICUS PARTIAL MRNA FOR IMMUNOGLOBULIN LIGHT CHAIN VARIABLE REGION, (IGLV GENE), MAB192

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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: 2.36 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 289 K / pH: 7.5
Details: 12 MG/ML FAB192, 18% W/V PEG6000, 150 MM NACL, 100 MM BIS-TRIS/HCL, PH 7.5, 2 MM EDTA, AT 16 DEG. C, temperature 289K
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
218 %(w/v)PEG60001reservoir
3150 mM1reservoirNaCl
4100 mMbis-Tris-HCl1reservoir
52 mMEDTA1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
DetectorDate: Jul 1, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 26381 / % possible obs: 76.1 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 42.8 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 25.45
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 9.12 / % possible all: 51.9
Reflection
*PLUS
Num. measured all: 118352
Reflection shell
*PLUS
% possible obs: 51.9 %

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Processing

Software
NameVersionClassification
XDSdata scaling
AUTOMARdata reduction
X-PLORmodel building
X-PLOR3.8refinement
XDSdata reduction
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CGR

2cgr


Resolution: 2.4→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.304 1288 4.9 %RANDOM
Rwork0.196 ---
obs0.196 26381 76.1 %-
Displacement parametersBiso mean: 37 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6506 0 0 209 6715
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d30.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.81
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.621.5
X-RAY DIFFRACTIONx_mcangle_it4.082
X-RAY DIFFRACTIONx_scbond_it3.962
X-RAY DIFFRACTIONx_scangle_it5.32.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.389 131 4.4 %
Rwork0.352 2815 -
obs--51.9 %
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg30.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.81

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