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- PDB-1m71: Crystal structure of a Monoclonal Fab Specific for Shigella Flexn... -

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Basic information

Entry
Database: PDB / ID: 1m71
TitleCrystal structure of a Monoclonal Fab Specific for Shigella Flexneri Y lipopolysaccharide
Components
  • heavy chain of the monoclonal antibody Fab SYA/J6
  • light chain of the monoclonal antibody Fab SYA/J6
KeywordsIMMUNE SYSTEM / Fab-carbohydrate interactions / anti-carbohydrate antibody / X-ray Diffracrion / Shigella O-antigen
Function / homology
Function and homology information


immunoglobulin mediated immune response / immunoglobulin complex / antigen binding / extracellular region / metal ion binding
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
If kappa light chain / Ig heavy chain V-III region J606
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsVyas, N.K. / Vyas, M.N. / Chervenak, M.C. / Johnson, M.A. / Pinto, B.M. / Bundle, D.R. / Quiocho, F.A.
Citation
Journal: Biochemistry / Year: 2002
Title: Molecular Recognition of Oligosaccharide Epitopes by a Monoclonal Fab Specific for Shigella flexneri Y Lipopolysaccharide: X-ray Structures and Thermodyanamics
Authors: Vyas, N.K. / Vyas, M.N. / Chervenak, M.C. / Johnson, M.A. / Pinto, B.M. / Bundle, D.R. / Quiocho, F.A.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Preliminary Crystallographic Analysis of a Fab Specific for the O-antigen of Shigella flexneri Cell Surface Lipopolysaccharide with and without Bound Saccharides
Authors: Vyas, N.K. / Vyas, M.N. / Meikkle, P.J. / Sinnott, B. / Pinto, B.M. / Bundle, D.R. / Quiocho, F.A.
History
DepositionJul 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE AT THE TIME OF PROCESSING, THIS SEQUENCE OF CHAIN A AND CHAIN B HAVE NOT YET BEEN ...SEQUENCE AT THE TIME OF PROCESSING, THIS SEQUENCE OF CHAIN A AND CHAIN B HAVE NOT YET BEEN DEPOSITED IN A SEQUENCE DATABASE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: light chain of the monoclonal antibody Fab SYA/J6
B: heavy chain of the monoclonal antibody Fab SYA/J6


Theoretical massNumber of molelcules
Total (without water)47,2652
Polymers47,2652
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-22 kcal/mol
Surface area20050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.700, 70.700, 202.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody light chain of the monoclonal antibody Fab SYA/J6


Mass: 23717.350 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balb/C / Cell: Plasmacytoma cell / Cell line: SYA/J6 hybridoma / Organ: Spleen / Production host: Escherichia coli (E. coli) / References: UniProt: A2NHM3*PLUS
#2: Antibody heavy chain of the monoclonal antibody Fab SYA/J6


Mass: 23547.361 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: Balb/C / Cell: Plasmacytoma cell / Cell line: SYA/J6 hybridoma / Organ: Spleen / Production host: Escherichia coli (E. coli) / References: UniProt: P01801*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.52 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: MPD, potassium phosphate, pH 6.5, VAPOR DIFFUSION, temperature 277K
Crystal grow
*PLUS
Details: Vyas, M.N., (1993) J. Mol. Biol., 231, 133.

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Data collection

DiffractionMean temperature: 281 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Jun 2, 1990
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 10392 / % possible obs: 77.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.5 / Redundancy: 6 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.116 / Rsym value: 0.08 / Net I/σ(I): 5
Reflection shellResolution: 2.8→2.97 Å / Num. unique all: 1236 / % possible all: 59.9
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. measured all: 108812
Reflection shell
*PLUS
% possible obs: 59.9 %

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Processing

Software
NameVersionClassification
Weissenbergdata collection
WEISdata reduction
MERLOTphasing
CNS1refinement
WEISSENBERGdata reduction
WEISdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MPC

1mpc


Resolution: 2.8→19.76 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 38035.32 / Data cutoff high rms absF: 38035.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 1.5 / Stereochemistry target values: Engh & Huber
Details: Author states residues 127-135 of chain B is part of a disordered segment, Bulk Solvent Model Used.
RfactorNum. reflection% reflectionSelection details
Rfree0.291 551 5.3 %RANDOM
Rwork0.223 ---
all-10392 --
obs-10392 77.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.201803 e/Å3
Displacement parametersBiso mean: 17.4 Å2
Baniso -1Baniso -2Baniso -3
1-5.55 Å20 Å20 Å2
2--5.55 Å20 Å2
3----11.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.86 Å0.79 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3323 0 0 62 3385
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it0.841.5
X-RAY DIFFRACTIONc_mcangle_it1.382
X-RAY DIFFRACTIONc_scbond_it0.512
X-RAY DIFFRACTIONc_scangle_it0.932.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.41 67 5.1 %
Rwork0.375 1236 -
obs--59.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.292
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95
LS refinement shell
*PLUS
Rfactor Rfree: 0.41

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