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- PDB-3c5s: Crystal Structure of monoclonal Fab F22-4 specific for Shigella f... -

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Basic information

Entry
Database: PDB / ID: 3c5s
TitleCrystal Structure of monoclonal Fab F22-4 specific for Shigella flexneri 2a O-Ag
Components
  • Fab F22-4 heavy chain
  • Fab F22-4 light chain
KeywordsIMMUNE SYSTEM / Antibody / O-Antigen / LPS / Shigella flexneri
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionFeb 1, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: 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 / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_end

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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


Theoretical massNumber of molelcules
Total (without water)95,5534
Polymers95,5534
Non-polymers00
Water7,224401
1
A: Fab F22-4 light chain
B: Fab F22-4 heavy chain


Theoretical massNumber of molelcules
Total (without water)47,7762
Polymers47,7762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-22 kcal/mol
Surface area19160 Å2
MethodPISA
2
C: Fab F22-4 light chain
D: Fab F22-4 heavy chain


Theoretical massNumber of molelcules
Total (without water)47,7762
Polymers47,7762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-22 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.260, 59.830, 74.380
Angle α, β, γ (deg.)77.530, 83.970, 80.890
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody Fab F22-4 light chain


Mass: 24141.777 Da / Num. of mol.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: BALB/c
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 401 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE DATABASE FOR CHAINS A,C RESIDUES 1-107 IS CAH04481.2, AND FOR CHAINS B,D RESIDUES 1- ...THE SEQUENCE DATABASE FOR CHAINS A,C RESIDUES 1-107 IS CAH04481.2, AND FOR CHAINS B,D 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), AND BETWEEN DATABASE SEQUENCE CAH04480.1 AND THIS ENTRY AT POSITION VAL 4 (CHAINS B,D). 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: 2.12 Å3/Da / Density % sol: 41.88 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 24% PEG 2000 MME, 190mM MgCl2, 50mM sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 14, 2001 / Details: bent mirror
RadiationMonochromator: Diamond(111), Ge(220), sagitally focusing Ge(220), multilayer
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→72.36 Å / Num. all: 50673 / Num. obs: 50673 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 7
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.144 / Mean I/σ(I) obs: 5.1 / Num. unique all: 7292 / Rsym value: 0.144 / % possible all: 94.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0003refinement
PDB_EXTRACT3.004data extraction
XDSdata scaling
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: VL/VH dimer: pdb entry 1ejo residues 2002L-2109L; pdb entry 1aj4 residues 1H-99H; CL/CH dimer: pdb entry 1f11 residues 108A-211A and 114B-227B.

1ejo

1aj4

1f11

108a

211a

114b

227b


Resolution: 2→72.36 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.907 / SU B: 5.549 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.229 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1307 2.6 %RANDOM
Rwork0.199 ---
all0.201 50671 --
obs0.201 50671 95.76 %-
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: 28.559 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å21.93 Å2-1.83 Å2
2---0.4 Å2-0.88 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2→72.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6482 0 0 401 6883
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226652
X-RAY DIFFRACTIONr_bond_other_d0.0010.025812
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.9529059
X-RAY DIFFRACTIONr_angle_other_deg0.783313604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.545833
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.88723.846260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.807151074
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2611530
X-RAY DIFFRACTIONr_chiral_restr0.0850.21022
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027332
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021316
X-RAY DIFFRACTIONr_nbd_refined0.1880.21124
X-RAY DIFFRACTIONr_nbd_other0.1860.25885
X-RAY DIFFRACTIONr_nbtor_refined0.1810.23156
X-RAY DIFFRACTIONr_nbtor_other0.0870.24049
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2380
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2480.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2560.222
X-RAY DIFFRACTIONr_mcbond_it1.39324460
X-RAY DIFFRACTIONr_mcbond_other0.26821700
X-RAY DIFFRACTIONr_mcangle_it2.12336815
X-RAY DIFFRACTIONr_scbond_it1.78132789
X-RAY DIFFRACTIONr_scangle_it2.39742244
LS refinement shellResolution: 2→2.026 Å / Total num. of bins used: 40
RfactorNum. reflection% reflection
Rfree0.411 35 -
Rwork0.246 1737 -
all-1772 -
obs-1772 91.15 %

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