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- PDB-1m7i: CRYSTAL STRUCTURE OF A MONOCLONAL FAB SPECIFIC FOR SHIGELLA FLEXN... -

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Basic information

Entry
Database: PDB / ID: 1m7i
TitleCRYSTAL STRUCTURE OF A MONOCLONAL FAB SPECIFIC FOR SHIGELLA FLEXNERI Y LIPOPOLYSACCHARIDE COMPLEXED WITH A PENTASACCHARIDE
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 / and anti-carbohydrate antibody
Function / homology
Function and homology information


immunoglobulin mediated immune response / immunoglobulin complex / antigen binding / adaptive immune response / extracellular region / metal ion binding / plasma membrane
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: 2.5 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. / Chervenak, M.C. / Johnson, M.A. / 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: Non-polymer description / Version format compliance
Revision 1.3Oct 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 / 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 / _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 2.1Nov 6, 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)48,0853
Polymers47,2652
Non-polymers8201
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5080 Å2
ΔGint1 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.510, 70.510, 203.100
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: Polysaccharide alpha-L-rhamnopyranose-(1-2)-alpha-L-rhamnopyranose-(1-3)-alpha-L-rhamnopyranose-(1-3)-2-acetamido- ...alpha-L-rhamnopyranose-(1-2)-alpha-L-rhamnopyranose-(1-3)-alpha-L-rhamnopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-methyl 6-deoxy-alpha-L-rhamnopyranoside


Type: oligosaccharide / Mass: 819.798 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LRhapa1-2LRhapa1-3LRhapa1-3DGlcpNAcb1-2LRhap[1Me]a1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2211m-1a_1-5_1*OC][a2122h-1b_1-5_2*NCC/3=O][a2211m-1a_1-5]/1-2-3-3-3/a2-b1_b3-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-L-Rhap]{[(2+1)][b-D-GlcpNAc]{[(3+1)][a-L-Rhap]{[(3+1)][a-L-Rhap]{[(2+1)][a-L-Rhap]{}}}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.67 Å3/Da / Density % sol: 53.92 %
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: FUJI / Detector: IMAGE PLATE / Date: Jun 2, 1990 / Details: hoton Factory BL6A2
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 14764 / Num. obs: 14375 / % possible obs: 79.6 % / Observed criterion σ(I): 1.5 / Redundancy: 6.5 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.075 / Net I/σ(I): 10
Reflection shellResolution: 2.5→2.66 Å / Num. unique all: 737 / % possible all: 55.2
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. measured all: 108148
Reflection shell
*PLUS
% possible obs: 55.2 %

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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: 2.5→20 Å / Rfactor Rfree error: 0.01 / 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
Rfree0.282 737 5 %RANDOM
Rwork0.22 ---
all0.22 14764 --
obs0.22 14375 79.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.142 Å2 / ksol: 0.302051 e/Å3
Displacement parametersBiso mean: 35.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.36 Å20 Å20 Å2
2--4.36 Å20 Å2
3----8.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3323 0 56 170 3549
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg3.1
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_improper_angle_d2.68
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.41 74 -
Rwork0.389 0 -
obs-1569 55.2 %
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: 2.5 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.279 / Rfactor Rwork: 0.207
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_deg26.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.68
LS refinement shell
*PLUS
Rfactor Rfree: 0.411

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