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- PDB-1mfe: RECOGNITION OF A CELL-SURFACE OLIGO-SACCHARIDE OF PATHOGENIC SALM... -

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Basic information

Entry
Database: PDB / ID: 1mfe
TitleRECOGNITION OF A CELL-SURFACE OLIGO-SACCHARIDE OF PATHOGENIC SALMONELLA BY AN ANTIBODY FAB FRAGMENT
Components
  • IGG1-LAMBDA SE155-4 FAB (HEAVY CHAIN)
  • IGG1-LAMBDA SE155-4 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsCygler, M.
CitationJournal: Science / Year: 1991
Title: Recognition of a cell-surface oligosaccharide of pathogenic Salmonella by an antibody Fab fragment.
Authors: Cygler, M. / Rose, D.R. / Bundle, D.R.
History
DepositionOct 25, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Polymer sequence
Category: chem_comp / entity_poly ...chem_comp / entity_poly / pdbx_database_status / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can ..._chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.process_site / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 3.0Jul 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.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.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGG1-LAMBDA SE155-4 FAB (LIGHT CHAIN)
H: IGG1-LAMBDA SE155-4 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1523
Polymers46,6792
Non-polymers4721
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-11 kcal/mol
Surface area18450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.300, 128.600, 79.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO L 144 / 2: CIS PROLINE - PRO H 402 / 3: CIS PROLINE - PRO H 404 / 4: CIS PROLINE - PRO H 444

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Components

#1: Antibody IGG1-LAMBDA SE155-4 FAB (LIGHT CHAIN)


Mass: 23108.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 387376
#2: Antibody IGG1-LAMBDA SE155-4 FAB (HEAVY CHAIN)


Mass: 23570.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 208365
#3: Polysaccharide alpha-D-galactopyranose-(1-2)-[alpha-D-Abequopyranose-(1-3)]alpha-D-mannopyranose


Type: oligosaccharide / Mass: 472.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpa1-2[DAbea1-3]DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a1122h-1a_1-5][a2112h-1a_1-5][a2d12m-1a_1-5]/1-2-3/a2-b1_a3-c1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(2+1)][a-D-Galp]{}[(3+1)][a-D-3-deoxy-Fucp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.48 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Details: taken from Rose, D.R. et al. (1990). J. Mol. Biol., 215, 489-492.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
215 %(w/v)PEG80001reservoir
350 mMTris-HCl1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.05 Å / % possible obs: 98 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.185 / Rfactor obs: 0.185 / Highest resolution: 2 Å
Details: THREE DISULFIDE BRIDGES WERE REFINED ASSUMING TWO ALTERNATIVE CONFORMATIONS: 22 - 90, 272 - 346, AND 395 - 450.
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3220 0 32 184 3436
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg2.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.05 Å / Lowest resolution: 6 Å / Num. reflection obs: 24312 / σ(I): 2 / Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.9

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