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- PDB-3bz4: Crystal structure of Fab F22-4 in complex with a Shigella flexner... -

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Basic information

Entry
Database: PDB / ID: 3bz4
TitleCrystal structure of Fab F22-4 in complex with a Shigella flexneri 2a O-Ag decasaccharide
Components
  • Fab F22-4 heavy chain
  • Fab F22-4 light chain
KeywordsIMMUNE SYSTEM / O-Antigen / LPS / Shigella flexneri / antibody complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PALLADIUM ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSaul, F.A. / Vulliez-le-Normand, B. / Bentley, G.A.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structures of synthetic O-antigen fragments from serotype 2a Shigella flexneri in complex with a protective monoclonal antibody
Authors: Vulliez-Le Normand, B. / Saul, F.A. / Phalipon, A. / Belot, F. / Guerreiro, C. / Mulard, L.A. / Bentley, G.A.
History
DepositionJan 17, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_conn_type / struct_ref_seq / 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_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _struct_conn.conn_type_id / _struct_conn.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.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_type.id / _struct_ref_seq.db_align_end
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: 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_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab F22-4 light chain
B: Fab F22-4 heavy chain
C: Fab F22-4 light chain
D: Fab F22-4 heavy chain
E: Fab F22-4 light chain
F: Fab F22-4 heavy chain
G: Fab F22-4 light chain
H: Fab F22-4 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,88613
Polymers191,1068
Non-polymers6,7815
Water44,5872475
1
A: Fab F22-4 light chain
B: Fab F22-4 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4453
Polymers47,7762
Non-polymers1,6691
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6240 Å2
ΔGint22 kcal/mol
Surface area19360 Å2
MethodPISA
2
C: Fab F22-4 light chain
D: Fab F22-4 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4453
Polymers47,7762
Non-polymers1,6691
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint23 kcal/mol
Surface area19340 Å2
MethodPISA
3
E: Fab F22-4 light chain
F: Fab F22-4 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5514
Polymers47,7762
Non-polymers1,7752
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint20 kcal/mol
Surface area19240 Å2
MethodPISA
4
G: Fab F22-4 light chain
H: Fab F22-4 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4453
Polymers47,7762
Non-polymers1,6691
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint23 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.060, 137.600, 109.800
Angle α, β, γ (deg.)90.000, 95.150, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
Fab F22-4 light chain


Mass: 24141.777 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/c
#2: Antibody
Fab F22-4 heavy chain


Mass: 23634.598 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/c
#3: Polysaccharide
alpha-L-rhamnopyranose-(1-2)-alpha-L-rhamnopyranose-(1-3)-[alpha-D-glucopyranose-(1-4)]alpha-L- ...alpha-L-rhamnopyranose-(1-2)-alpha-L-rhamnopyranose-(1-3)-[alpha-D-glucopyranose-(1-4)]alpha-L-rhamnopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-L-rhamnopyranose-(1-2)-alpha-L-rhamnopyranose-(1-3)-[alpha-D-glucopyranose-(1-4)]alpha-L-rhamnopyranose-(1-3)-2-aminoethyl 2-acetamido-2-deoxy-beta-D-glucopyranoside


Type: oligosaccharide / Mass: 1668.595 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/4,10,9/[a2122h-1b_1-5_1*OCCN_2*NCC/3=O][a2211m-1a_1-5][a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5]/1-2-2-2-3-2-2-2-4-4/a3-b1_b3-c1_b4-j1_c2-d1_d2-e1_e3-f1_f3-g1_f4-i1_g2-h1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-GlcpNAc]{[(3+1)][a-L-Rhap]{[(3+1)][a-L-Rhap]{[(2+1)][a-L-Rhap]{[(2+1)][b-D-GlcpNAc]{[(3+1)][a-L-Rhap]{[(3+1)][a-L-Rhap]{[(2+1)][a-L-Rhap]{}}[(4+1)][a-D-Glcp]{}}}}}[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-PD / PALLADIUM ION / Palladium


Mass: 106.420 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pd
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2475 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsDECASACCHARIDE CORRESPONDING TO TWO SHIGELLA FLEXNERI SEROTYPE 2A O-ANTIGEN REPEATING UNITS
Sequence detailsTHE SEQUENCE DATABASE FOR CHAINS A,C,E,G RESIDUES 1-107 IS CAH04481.2, AND FOR CHAINS B,D,F,H ...THE SEQUENCE DATABASE FOR CHAINS A,C,E,G RESIDUES 1-107 IS CAH04481.2, AND FOR CHAINS B,D,F,H RESIDUES 1-113 IS CAH04480.1. RESIDUE NUMBERING OF ANTIBODY VARIABLE REGIONS FOLLOWS THE KABAT CONVENTION (E.A. KABAT, T.T. WU, H.M. PERRY, K.S. GOTTESMAN, C. FOELLER. SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST, 5TH ED. (1991). NIH PUBLICATION NO.91-3242, NATIONAL INSTITUTES OF HEALTH, BETHESDA, MD). DISCREPANCIES BETWEEN THE DATABASE SEQUENCE CAH04481.2 AND THIS PDB ENTRY OCCUR AT POSITIONS ASP 1, ILE 2, ALA 7, ALA 8, AND PHE 9 (CHAINS A,C,E,G), AND BETWEEN DATABASE SEQUENCE CAH04480.1 AND THIS ENTRY AT POSITION VAL 4 (CHAINS B,D,F, H). THESE N-TERMINAL SEQUENCE DISCREPANCIES ARE DUE TO THE PRIMERS USED FOR NUCLEOTIDE SEQUENCE DETERMINATION.

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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: 53.41 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 25% PEG 5000 MMe, 0.2M Li2SO4, 0.1M Tris, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 17, 2006 / Details: bent mirror
RadiationMonochromator: Diamond (111), Ge (220) toroidal focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.8→47.946 Å / Num. all: 182390 / Num. obs: 182390 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 5.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 1.1 / Num. unique all: 26443 / Rsym value: 0.622 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0003refinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3c5s; chains C and D

3c5s


Resolution: 1.8→47.92 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.939 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2708 1.5 %RANDOM
Rwork0.176 ---
all0.177 182354 --
obs0.177 182354 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.808 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å2-0.22 Å2
2--1.62 Å20 Å2
3----1.27 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13121 0 449 2475 16045
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02214019
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212198
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.99219164
X-RAY DIFFRACTIONr_angle_other_deg0.778328449
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.59451692
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.79423.769536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.052152203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.541565
X-RAY DIFFRACTIONr_chiral_restr0.0860.22280
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214950
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022695
X-RAY DIFFRACTIONr_nbd_refined0.1920.22198
X-RAY DIFFRACTIONr_nbd_other0.1850.212299
X-RAY DIFFRACTIONr_nbtor_refined0.1770.26711
X-RAY DIFFRACTIONr_nbtor_other0.0830.28380
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.21925
X-RAY DIFFRACTIONr_xyhbond_nbd_other00.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1540.277
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.299
X-RAY DIFFRACTIONr_symmetry_hbond_other0.1770.21
X-RAY DIFFRACTIONr_mcbond_it1.35829009
X-RAY DIFFRACTIONr_mcbond_other0.2923445
X-RAY DIFFRACTIONr_mcangle_it2.001313834
X-RAY DIFFRACTIONr_scbond_it1.90536194
X-RAY DIFFRACTIONr_scangle_it2.56645329
LS refinement shellResolution: 1.8→1.823 Å / Total num. of bins used: 40
RfactorNum. reflection% reflection
Rfree0.278 91 -
Rwork0.257 6631 -
all-6722 -
obs-6722 99.19 %

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