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- PDB-3ggw: Crystal Structure of FAB F22-4 in complex with a Carbohydrate-mim... -

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Basic information

Entry
Database: PDB / ID: 3ggw
TitleCrystal Structure of FAB F22-4 in complex with a Carbohydrate-mimetic peptide
Components
  • FAB F22-4 HEAVY CHAIN
  • FAB F22-4 LIGHT CHAIN
  • PEPTIDE B1
KeywordsIMMUNE SYSTEM / PEPTIDE-CARBOHYDRATE MIMICRY / LPS / SHIGELLA FLEXNERI / ANTIBODY COMPLEX
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSaul, F.A. / Vulliez-Le Normand, B. / Bentley, G.A.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural Mimicry of O-Antigen by a Peptide Revealed in a Complex with an Antibody Raised against Shigella flexneri Serotype 2a
Authors: Theillet, F.-X. / Saul, F.A. / Vulliez-Le Normand, B. / Hoos, S. / Felici, F. / Weintraub, A. / Mulard, L.A. / Phalipon, A. / Delepierre, M. / Bentley, G.A.
History
DepositionMar 2, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 12, 2014Group: Derived calculations
Revision 1.3Nov 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
Revision 1.4Nov 13, 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

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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: PEPTIDE B1
F: PEPTIDE B1


Theoretical massNumber of molelcules
Total (without water)98,7846
Polymers98,7846
Non-polymers00
Water14,214789
1
A: FAB F22-4 LIGHT CHAIN
B: FAB F22-4 HEAVY CHAIN
E: PEPTIDE B1


Theoretical massNumber of molelcules
Total (without water)49,3923
Polymers49,3923
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-28 kcal/mol
Surface area19980 Å2
MethodPISA
2
C: FAB F22-4 LIGHT CHAIN
D: FAB F22-4 HEAVY CHAIN
F: PEPTIDE B1


Theoretical massNumber of molelcules
Total (without water)49,3923
Polymers49,3923
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-27 kcal/mol
Surface area20030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.880, 69.530, 110.190
Angle α, β, γ (deg.)90.00, 97.71, 90.00
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.: 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: Protein/peptide PEPTIDE B1


Mass: 1615.784 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: SYNTHETIC DODECAPEPTIDE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 789 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 6000, 50mM IMIDAZOLE, PH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 21, 2006 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 1.7→47.97 Å / Num. all: 107480 / Num. obs: 107480 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 21.24 Å2 / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 13.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.724 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.724 / % possible all: 96.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0003refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C5S

3c5s


Resolution: 1.7→47.97 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.591 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2146 2 %RANDOM
Rwork0.197 ---
all0.198 105405 --
obs0.198 105405 97.6 %-
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: 22.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å2-0.13 Å2
2--0.94 Å20 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6795 0 0 789 7584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0227018
X-RAY DIFFRACTIONr_bond_other_d0.0060.026099
X-RAY DIFFRACTIONr_angle_refined_deg1.591.9519571
X-RAY DIFFRACTIONr_angle_other_deg0.824314303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg17.7515886
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42324.093281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.604151141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9151529
X-RAY DIFFRACTIONr_chiral_restr0.0930.21073
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027751
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021390
X-RAY DIFFRACTIONr_nbd_refined0.2170.21143
X-RAY DIFFRACTIONr_nbd_other0.2040.25895
X-RAY DIFFRACTIONr_nbtor_refined0.1830.23333
X-RAY DIFFRACTIONr_nbtor_other0.0870.23889
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2634
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0840.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2870.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.82925578
X-RAY DIFFRACTIONr_mcbond_other0.32621785
X-RAY DIFFRACTIONr_mcangle_it2.01337148
X-RAY DIFFRACTIONr_scbond_it2.32333171
X-RAY DIFFRACTIONr_scangle_it2.84142413
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.72 Å / Total num. of bins used: 40
RfactorNum. reflection% reflection
Rfree0.341 94 -
Rwork0.273 3858 -
obs--96.2 %

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