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- PDB-5dq9: Structure of S55-3 Fab in complex with Lipid A -

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Basic information

Entry
Database: PDB / ID: 5dq9
TitleStructure of S55-3 Fab in complex with Lipid A
Components
  • MAb 44B1 light chain
  • S55-3 Fab (IgG2b) heavy chain
KeywordsIMMUNE SYSTEM / antibody / Fab / complex / carbohydrate
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsHaji-Ghassemi, O. / Evans, S.V.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Lipid A-antibody structures reveal a widely-utilized pocket specific for negatively charged groups derived from from unrelated V-genes
Authors: Haji-Ghassemi, O. / Muller-Loennies, S. / Rodriguez, T. / Brade, L. / Kosma, P. / Brade, H. / Evans, S.V.
History
DepositionSep 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
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_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_oper_list / pdbx_struct_special_symmetry / struct_asym / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_special_symmetry.label_asym_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 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: S55-3 Fab (IgG2b) heavy chain
B: MAb 44B1 light chain
C: S55-3 Fab (IgG2b) heavy chain
D: MAb 44B1 light chain
H: S55-3 Fab (IgG2b) heavy chain
L: MAb 44B1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,28711
Polymers142,4636
Non-polymers1,8245
Water8,701483
1
A: S55-3 Fab (IgG2b) heavy chain
B: MAb 44B1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0723
Polymers47,4882
Non-polymers5841
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-19 kcal/mol
Surface area19280 Å2
MethodPISA
2
C: S55-3 Fab (IgG2b) heavy chain
D: MAb 44B1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1074
Polymers47,4882
Non-polymers6202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-19 kcal/mol
Surface area18980 Å2
MethodPISA
3
H: S55-3 Fab (IgG2b) heavy chain
L: MAb 44B1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1074
Polymers47,4882
Non-polymers6202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-32 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)338.121, 52.865, 75.391
Angle α, β, γ (deg.)90.000, 100.950, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-301-

CL

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22H
13B
23D
14B
24L
15C
25H
16D
26L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 222
2010C1 - 222
1020A1 - 222
2020H1 - 222
1030B1 - 215
2030D1 - 215
1040B1 - 215
2040L1 - 215
1050C1 - 222
2050H1 - 222
1060D1 - 214
2060L1 - 214

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Antibody S55-3 Fab (IgG2b) heavy chain


Mass: 23382.039 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse)
#2: Antibody MAb 44B1 light chain


Mass: 24105.566 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse)
#3: Polysaccharide 2-acetamido-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-1-O-phosphono- ...2-acetamido-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 584.361 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5_1*OPO/3O/3=O_2*NCC/3=O][a2122h-1b_1-5_2*NCC/3=O_4*OPO/3O/3=O]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][P]{[(0+1)][a-D-GlcpNAc]{[(6+1)][b-D-GlcpNAc]{[(4+0)][P]{}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 483 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: 1M LiCl, 0.1M citric acid, and 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9794 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Apr 30, 2013 / Details: OSMIC BLUE MIRRORS
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. obs: 94048 / % possible obs: 98.7 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.092 / Χ2: 1.064 / Net I/av σ(I): 14.362 / Net I/σ(I): 9 / Num. measured all: 385955
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.95-2.024.20.57792940.99298.7
2.02-2.14.20.43293481.08598.7
2.1-2.24.20.34493521.0898.7
2.2-2.314.20.28593471.0898.9
2.31-2.464.20.23693391.06898.9
2.46-2.654.20.17994031.06998.9
2.65-2.914.10.13294461.07398.9
2.91-3.3340.09693741.03998.4
3.33-4.23.80.06494451.09298.2
4.2-253.80.0597001.06198.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ODS

4ods


Resolution: 1.95→25 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2569 / WRfactor Rwork: 0.2226 / FOM work R set: 0.8071 / SU B: 4.548 / SU ML: 0.13 / SU R Cruickshank DPI: 0.1978 / SU Rfree: 0.1671 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.198 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2453 4730 5 %RANDOM
Rwork0.2122 ---
obs0.2139 89318 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.18 Å2 / Biso mean: 38.843 Å2 / Biso min: 8.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.75 Å2
2---0.71 Å20 Å2
3---0.37 Å2
Refinement stepCycle: final / Resolution: 1.95→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9801 0 113 484 10398
Biso mean--20.07 37.22 -
Num. residues----1292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0210147
X-RAY DIFFRACTIONr_bond_other_d0.0050.029153
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.96213827
X-RAY DIFFRACTIONr_angle_other_deg1.1093.00521211
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55551281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59924.03397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.794151577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9241548
X-RAY DIFFRACTIONr_chiral_restr0.1090.21569
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111406
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022246
X-RAY DIFFRACTIONr_mcbond_it2.2933.7795157
X-RAY DIFFRACTIONr_mcbond_other2.2933.7795156
X-RAY DIFFRACTIONr_mcangle_it3.4415.656427
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A111570.1
12C111570.1
21A112250.1
22H112250.1
31B113560.12
32D113560.12
41B111360.12
42L111360.12
51C114180.09
52H114180.09
61D111080.11
62L111080.11
LS refinement shellResolution: 1.952→2.003 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 293 -
Rwork0.257 6279 -
all-6572 -
obs--93.82 %

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