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- PDB-1m7d: Crystal structure of a Monoclonal Fab Specific for Shigella flexn... -

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Basic information

Entry
Database: PDB / ID: 1m7d
TitleCrystal structure of a Monoclonal Fab Specific for Shigella flexneri Y Lipopolysaccharide complexed with a trisaccharide
Components
  • heavy chain of the monoclonal antibody Fab SYA/J6
  • light chain of the monoclonal antibody Fab SYA/J6
KeywordsIMMUNE SYSTEM / Fab-carbohydrate interactions / Shigella O-antigen / anti-carbohydrate antibody
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / 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: 2.3 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 Thermodynamics
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 Lipoplysacharide with and and without Bound Saccharides
Authors: Vyas, N.K. / Vyas, M.N. / Meikele, P.J. / Sinnott, B. / Pinto, B.M. / Bundle, D.R. / Quiocho, F.A.
History
DepositionJul 19, 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 16, 2011Group: Atomic model
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7763
Polymers47,2652
Non-polymers5121
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-7 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.000, 71.000, 198.000
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-229-

HOH

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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: Polysaccharide alpha-L-rhamnopyranose-(1-3)-alpha-L-Olivopyranose-(1-3)-methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside


Type: oligosaccharide / Mass: 511.517 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LRhapa1-3LOlia1-3DGlcpNAc[1Me]b1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_1*OC_2*NCC/3=O][ad211m-1a_1-5][a2211m-1a_1-5]/1-2-3/a3-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-GlcpNAc]{[(3+1)][a-L-2,6-deoxy-Glcp]{[(3+1)][a-L-Rhap]{}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.64 Å3/Da / Density % sol: 53.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: MPD, potassium phoshate, , 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: 2.3→20 Å / Num. obs: 17923 / % possible obs: 76.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.5 / Redundancy: 5 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.06 / Net I/σ(I): 7.5
Reflection shellResolution: 2.3→2.44 Å / Num. unique all: 112 / % possible all: 51.3
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. measured all: 112922
Reflection shell
*PLUS
% possible obs: 51.3 %

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Processing

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

1mcp


Resolution: 2.3→19.98 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 76031.28 / Data cutoff high rms absF: 76031.28 / 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.279 869 4.8 %RANDOM
Rwork0.216 ---
all-17923 --
obs-17923 76.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.674 Å2 / ksol: 0.348726 e/Å3
Displacement parametersBiso mean: 40.2 Å2
Baniso -1Baniso -2Baniso -3
1-4.59 Å20 Å20 Å2
2--4.59 Å20 Å2
3----9.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 35 121 3478
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_improper_angle_d0.92
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.327 114 5.8 %
Rwork0.285 1844 -
obs--51.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3PARAM1NKV.CHOTOPH1NKV.CHO
Refinement
*PLUS
Highest resolution: 2.3 Å / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.214 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92

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