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- PDB-1pz5: Structural basis of peptide-carbohydrate mimicry in an antibody c... -

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Basic information

Entry
Database: PDB / ID: 1pz5
TitleStructural basis of peptide-carbohydrate mimicry in an antibody combining site
Components
  • Heavy chain of Fab (SYA/J6)
  • Light chain of Fab (SYA/J6)
  • Octapeptide (MDWNMHAA)
KeywordsIMMUNE SYSTEM / Antibody-antigen structure / peptide-carbohydrate mimicry / vaccine design
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / metal ion binding
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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
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: 1.8 Å
AuthorsVyas, N.K. / Vyas, M.N. / Chervenak, M.C. / Bundle, D.R. / Pinto, B.M. / Quiocho, F.A.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Structural basis of peptide-carbohydrate mimicry in an antibody combining site.
Authors: Vyas, N.K. / Vyas, M.N. / Chervenak, M.C. / Bundle, D.R. / Pinto, B.M. / Quiocho, F.A.
#1: Journal: Biochemistry / Year: 2002
Title: Molecular recognition of oligosaccharide epitopes by a monoclonal Fab sepcific for Shigella flexneri Y lipopolysaccharide: X-ray structures and thermodynamics.
Authors: Vyas, N.K. / Vyas, M.N. / Chervenak, M.C. / Johnson, M.A. / Pinto, B.M. / Bundle, D.R. / Quiocho, F.A.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Preliminary crystallographic analysis of a Fab specific for the O-antigen of Shigella flexneri cell surface lipopoysaccharide with and without bound saccharides
Authors: Vyas, M.N. / Vyas, N.K. / Meikle, P.J. / Sinnott, B. / Pinto, B.M. / Bundle, D.R. / Quiocho, F.A.
History
DepositionJul 9, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 16, 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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE No database reference sequence was found for the proteins in this structure at the time of ...SEQUENCE No database reference sequence was found for the proteins in this structure at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Light chain of Fab (SYA/J6)
B: Heavy chain of Fab (SYA/J6)
C: Octapeptide (MDWNMHAA)


Theoretical massNumber of molelcules
Total (without water)48,2573
Polymers48,2573
Non-polymers00
Water9,206511
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-30 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.310, 69.310, 198.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-232-

HOH

21B-447-

HOH

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Components

#1: Antibody Light chain of Fab (SYA/J6)


Mass: 23717.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: spleen / Strain: BALB/C / References: UniProt: A2NHM3*PLUS
#2: Antibody Heavy chain of Fab (SYA/J6)


Mass: 23563.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Organ: spleen / Strain: BALB/C / References: UniProt: P01801*PLUS
#3: Protein/peptide Octapeptide (MDWNMHAA)


Mass: 976.110 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The octapeptide was synthesized as its carboxamide (Alberta peptide Institure, Edmonton, Canada)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 2.47 Å3/Da / Density % sol: 50.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: MPD, potassium phoshphate, pH 6.5, VAPOR DIFFUSION, temperature 277.0K
Crystal grow
*PLUS
Details: Vyas, M.N., (1993) J. Mol. Biol., 231, 133.

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.948 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.948 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. all: 42148 / Num. obs: 42148 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 12.3 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 35.1
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.65 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 6.5 / Num. unique all: 2644 / Rsym value: 0.12 / % possible all: 58.9
Reflection
*PLUS
Redundancy: 4.02 % / Num. measured all: 169601
Reflection shell
*PLUS
% possible obs: 58.9 % / Num. unique obs: 2644 / Num. measured obs: 9660 / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1M71

1m71


Resolution: 1.8→19.97 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 4210 10.1 %RANDOM
Rwork0.219 ---
all0.219 42148 --
obs0.219 41694 90.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.9066 Å2 / ksol: 0.352158 e/Å3
Displacement parametersBiso mean: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å20 Å20 Å2
2--1.61 Å20 Å2
3----3.21 Å2
Refine analyzeLuzzati coordinate error free: 0.27 Å / Luzzati sigma a free: 0.16 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3391 0 0 511 3902
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it0.641.5
X-RAY DIFFRACTIONc_mcangle_it0.862
X-RAY DIFFRACTIONc_scbond_it0.612
X-RAY DIFFRACTIONc_scangle_it0.882.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.268 464 9.7 %
Rwork0.235 4322 -
obs-2600 63.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3TOPH1NKV.CHO
Refinement
*PLUS
Highest resolution: 1.8 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
LS refinement shell
*PLUS
Highest resolution: 1.8 Å / Rfactor Rwork: 0.233

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