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- PDB-1f4y: CRYSTAL STRUCTURE OF AN ANTI-CARBOHYDRATE ANTIBODY DIRECTED AGAIN... -

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Basic information

Entry
Database: PDB / ID: 1f4y
TitleCRYSTAL STRUCTURE OF AN ANTI-CARBOHYDRATE ANTIBODY DIRECTED AGAINST VIBRIO CHOLERAE O1 IN COMPLEX WITH ANTIGEN
Components
  • ANTIBODY S-20-4, FAB FRAGMENT, HEAVY CHAIN
  • ANTIBODY S-20-4, FAB FRAGMENT, LIGHT CHAIN
KeywordsIMMUNE SYSTEM / anti-carbohydrate antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsAlzari, P.M. / Souchon, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Crystal structure of an anti-carbohydrate antibody directed against Vibrio cholerae O1 in complex with antigen: molecular basis for serotype specificity.
Authors: Villeneuve, S. / Souchon, H. / Riottot, M.M. / Mazie, J.C. / Lei, P. / Glaudemans, C.P. / Kovac, P. / Fournier, J.M. / Alzari, P.M.
History
DepositionJun 10, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 26, 2016Group: Non-polymer description
Revision 1.4Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: 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 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: ANTIBODY S-20-4, FAB FRAGMENT, LIGHT CHAIN
H: ANTIBODY S-20-4, FAB FRAGMENT, HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3423
Polymers45,8012
Non-polymers5411
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-26 kcal/mol
Surface area18900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.690, 113.360, 45.580
Angle α, β, γ (deg.)90.00, 93.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody ANTIBODY S-20-4, FAB FRAGMENT, LIGHT CHAIN


Mass: 22527.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Secretion: ASCITES
#2: Antibody ANTIBODY S-20-4, FAB FRAGMENT, HEAVY CHAIN


Mass: 23274.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Secretion: ASCITES
#3: Polysaccharide 4,6-dideoxy-4-{[(2R)-2,4-dihydroxybutanoyl]amino}-2-O-methyl-alpha-D-mannopyranose-(1-2)-methyl 4,6- ...4,6-dideoxy-4-{[(2R)-2,4-dihydroxybutanoyl]amino}-2-O-methyl-alpha-D-mannopyranose-(1-2)-methyl 4,6-dideoxy-4-{[(2R)-2,4-dihydroxybutanoyl]amino}-alpha-D-mannopyranoside


Type: oligosaccharide / Mass: 540.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,4,3/[a1122m-1a_1-5_1*OC][a1122m-1a_1-5_2*OC][A2dh]/1-2-3-3/a2-b1_a4-d1*N*_b4-c1*N*WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-Rhap4N]{[(4+1)][<C4O3>]{}[(2+1)][a-D-Rhap2Me4N]{[(4+1)][<C4O3>]{}}}}LINUCSPDB-CARE
Has protein modificationY
Sequence detailsTHE ATOMIC COORDINATES IN THIS ENTRY FOLLOW A CORRELATIVE NUMBERING SCHEME. INSTEAD, KABAT ...THE ATOMIC COORDINATES IN THIS ENTRY FOLLOW A CORRELATIVE NUMBERING SCHEME. INSTEAD, KABAT NUMBERING SCHEME OF ANTIBODIES IS USED THROUGHOUT THE PNAS MANUSCRIPT.

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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: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 6000, sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
220 mMTris-HCl1drop
315-18 %PEG60001reservoir
450 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 20, 1999
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 9638 / Num. obs: 9638 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 45.4 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 8.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.296 / % possible all: 91.3
Reflection
*PLUS
Num. measured all: 27225
Reflection shell
*PLUS
% possible obs: 91.3 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: STRUCTURE OF THE UNLIGANDED FAB FRAGMENT

Resolution: 2.8→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.352 459 5 %random
Rwork0.226 ---
all-9435 --
obs-9435 --
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3194 0 37 0 3231
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.060.04
X-RAY DIFFRACTIONp_planar_d0.060.05
Software
*PLUS
Name: REFMAC / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rfree: 0.507 / Rfactor Rwork: 0.272

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