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- PDB-4ods: Unliganded Fab structure of lipid A-specific antibody S55-3 -

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Basic information

Entry
Database: PDB / ID: 4ods
TitleUnliganded Fab structure of lipid A-specific antibody S55-3
Components(S55-3 Fab (IgG2b) heavy chain) x 2
KeywordsIMMUNE SYSTEM / Carbohydrate binding
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å
AuthorsHaji-Ghassemi, O. / Evans, S.V.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis for Antibody Recognition of Lipid A: INSIGHTS TO POLYSPECIFICITY TOWARD SINGLE-STRANDED DNA.
Authors: Haji-Ghassemi, O. / Muller-Loennies, S. / Rodriguez, T. / Brade, L. / Kosma, P. / Brade, H. / Evans, S.V.
History
DepositionJan 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.4Sep 20, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: S55-3 Fab (IgG2b) heavy chain
L: S55-3 Fab (IgG2b) heavy chain


Theoretical massNumber of molelcules
Total (without water)47,4882
Polymers47,4882
Non-polymers00
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-23 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.611, 44.330, 85.362
Angle α, β, γ (deg.)90.00, 111.56, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 23382.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c
#2: Antibody S55-3 Fab (IgG2b) heavy chain


Mass: 24105.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.51 Å3/Da / Density % sol: 50.97 %
Crystal growTemperature: 289 K / pH: 9.5
Details: Drop: 0.05M Glycine, 4% (w/v) PEG 3350 Reservoir: 24% (w/v) PEG 3350, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002+ / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 6, 2011 / Details: OSMIC BLUE MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.94→79.39 Å / Num. obs: 33609 / % possible obs: 95.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 11.9
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.427 / % possible all: 92.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.5phasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FV FRAGMENT FROM PDB ENTRY 3S35, CONSTANT DOMAINS FROM PDB ENTRY 1NBV

3s35

1nbv


Resolution: 1.94→79.39 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.914 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.788 / SU ML: 0.133 / SU R Cruickshank DPI: 0.1889 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.189 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1677 5 %RANDOM
Rwork0.21 ---
obs0.212 33590 95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.08 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å2-0 Å2-0.63 Å2
2--3.3 Å2-0 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.94→79.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 0 240 3552
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023398
X-RAY DIFFRACTIONr_bond_other_d0.0020.023076
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.954626
X-RAY DIFFRACTIONr_angle_other_deg0.81337124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5025434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86824135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11415537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9621517
X-RAY DIFFRACTIONr_chiral_restr0.0920.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213864
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02761
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5582.591745
X-RAY DIFFRACTIONr_mcbond_other1.5582.591744
X-RAY DIFFRACTIONr_mcangle_it2.5133.8712176
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 112 -
Rwork0.304 2240 -
obs--90.88 %

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