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- PDB-3v0w: Crystal structure of Fab WN1 222-5 in complex with LPS -

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Basic information

Entry
Database: PDB / ID: 3v0w
TitleCrystal structure of Fab WN1 222-5 in complex with LPS
Components
  • WN1 222-5 Fab (IgG2a) heavy chain
  • WN1 222-5 Fab (IgG2a) light chain
KeywordsIMMUNE SYSTEM / Beta barrel / Antibody / Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.73 Å
AuthorsGomery, K. / Evans, S.V.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Antibody WN1 222-5 mimics Toll-like receptor 4 binding in the recognition of LPS.
Authors: Gomery, K. / Muller-Loennies, S. / Brooks, C.L. / Brade, L. / Kosma, P. / Di Padova, F. / Brade, H. / Evans, S.V.
History
DepositionDec 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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_validate_close_contact / struct_asym / struct_conn / 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_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: WN1 222-5 Fab (IgG2a) light chain
H: WN1 222-5 Fab (IgG2a) heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,64413
Polymers46,6792
Non-polymers2,96511
Water9,476526
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-108 kcal/mol
Surface area19170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.852, 101.852, 118.532
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody WN1 222-5 Fab (IgG2a) light chain


Mass: 23281.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: HYBRIDOMA / Strain: NZB
#2: Antibody WN1 222-5 Fab (IgG2a) heavy chain


Mass: 23397.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: HYBRIDOMA / Strain: NZB
#3: Polysaccharide 2-amino-2-deoxy-alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)- ...2-amino-2-deoxy-alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-2)-alpha-D-glucopyranose-(1-3)-[alpha-D-galactopyranose-(1-6)]alpha-D-glucopyranose-(1-3)-[L-glycero-alpha-D-manno-heptopyranose-(1-7)]4-O-phosphono-L-glycero-alpha-D-manno-heptopyranose-(1-3)-4-O-phosphono-L-glycero-alpha-D-manno-heptopyranose-(1-5)-[3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid


Type: oligosaccharide / Mass: 2004.548 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/6,10,9/[Aad1122h-2a_2-6][a11221h-1a_1-5_4*OPO/3O/3=O][a2122h-1a_1-5][a2122h-1a_1-5_2*N][a2112h-1a_1-5][a11221h-1a_1-5]/1-1-2-2-3-3-3-4-5-6/a4-b2_a5-c1_c3-d1_d3-e1_d7-j1_e3-f1_e6-i1_f2-g1_g2-h1WURCSPDB2Glycan 1.1.0
[][a-D-Kdop]{[(4+2)][a-D-Kdop]{}[(5+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(3+1)][a-D-Glcp]{[(3+1)][a-D-Glcp]{[(2+1)][a-D-Glcp]{[(2+1)][a-D-GlcpN]{}}}[(6+1)][a-D-Galp]{}}[(4+0)][P]{}}[(4+0)][P]{}}}LINUCSPDB-CARE
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 526 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsSUGARS H 301-310 ARE THE OBSERVED REGION OF THE NATURALLY OCCURING LIPOPOLYSACCHARIDE FROM THE ...SUGARS H 301-310 ARE THE OBSERVED REGION OF THE NATURALLY OCCURING LIPOPOLYSACCHARIDE FROM THE OUTER MEMBRANE OF GRAM-NEGATIVE BACTERIA

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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: 3.29 Å3/Da / Density % sol: 62.65 %
Crystal growTemperature: 289 K / Method: hanging drop / pH: 4.6
Details: Sodium acetate, Ammonium sulfate, pH 4.6, hanging drop, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 17, 2011 / Details: Vertical focussing mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.72→30 Å / Num. obs: 65161 / % possible obs: 97.9 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 15.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.72-1.784.30.256185.1
1.78-1.854.90.192198.8
1.85-1.9450.137199.5
1.94-2.045.10.098199.7
2.04-2.175.30.078199.8
2.17-2.335.50.07199.8
2.33-2.575.70.062199.7
2.57-2.945.70.04199.5
2.94-3.75.60.044198.8
3.7-305.60.033197.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
MxDCdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.73→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 1.795 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.231 3288 5.1 %RANDOM
Rwork0.182 ---
obs0.184 61638 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.73→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3244 0 183 526 3953
LS refinement shellResolution: 1.728→1.773 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 234 -
Rwork0.218 4366 -
obs--96.15 %

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