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- PDB-4z95: Fab structure of antibody S1-15 in complex with ssDNA DNA, 5'-5(d... -

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Basic information

Entry
Database: PDB / ID: 4z95
TitleFab structure of antibody S1-15 in complex with ssDNA DNA, 5'-5(dT)-p-3'
Components
  • S1-15 Fab (IgG2b) heavy chain
  • S1-15 Fab (IgG2b) light chain
KeywordsIMMUNE SYSTEM/DNA / antibody / Fab / carbohydrate / lipid A / DNA / IMMUNE SYSTEM / IMMUNE SYSTEM-DNA complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 Å
AuthorsHaji-Ghassemi, O. / Evans, S.V.
Funding support Canada, Austria, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)OGP0171356 Canada
FWFP22909 Austria
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
DepositionApr 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Aug 26, 2015Group: Database references
Revision 1.3Aug 23, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.type / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 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 1.7Oct 23, 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
H: S1-15 Fab (IgG2b) heavy chain
L: S1-15 Fab (IgG2b) light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2583
Polymers48,1632
Non-polymers951
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-32 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.761, 77.761, 156.525
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11H-486-

HOH

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Components

#1: Antibody S1-15 Fab (IgG2b) heavy chain


Mass: 24436.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c
#2: Antibody S1-15 Fab (IgG2b) light chain


Mass: 23727.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O
Compound detailsthe ligand used for crystallization was 5'-DTpDTpDTpDTpDTp-3', however only a phosphate could be ...the ligand used for crystallization was 5'-DTpDTpDTpDTpDTp-3', however only a phosphate could be confidently modeled due to lack of electron density.
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: 2.46 Å3/Da / Density % sol: 49.93 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris-HCl pH 8.5, 25% (v/v) PEG 550 MME

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 5, 2014 / Details: Vertical focusing mirror
RadiationMonochromator: DCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.79→25 Å / Num. all: 457680 / Num. obs: 43749 / % possible obs: 99.9 % / Redundancy: 9.9 % / Rsym value: 0.053 / Net I/σ(I): 37.7
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 10 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHASER2.5.6phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-2000v701c3data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ODT

4odt


Resolution: 1.79→25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.2437 / WRfactor Rwork: 0.2146 / FOM work R set: 0.7944 / SU B: 3.375 / SU ML: 0.103 / SU R Cruickshank DPI: 0.131 / SU Rfree: 0.1245 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2362 2269 4.9 %RANDOM
Rwork0.2028 ---
obs0.2045 43749 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 110.19 Å2 / Biso mean: 38.743 Å2 / Biso min: 19.81 Å2
Baniso -1Baniso -2Baniso -3
1-1.45 Å2-0 Å2-0 Å2
2--1.45 Å2-0 Å2
3----2.9 Å2
Refinement stepCycle: final / Resolution: 1.79→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3375 0 5 275 3655
Biso mean--49.2 41.93 -
Num. residues----440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.023467
X-RAY DIFFRACTIONr_bond_other_d0.0010.023119
X-RAY DIFFRACTIONr_angle_refined_deg1.3361.944720
X-RAY DIFFRACTIONr_angle_other_deg0.74837215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8515439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3324.113141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79715549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4531516
X-RAY DIFFRACTIONr_chiral_restr0.0790.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213931
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02795
X-RAY DIFFRACTIONr_mcbond_it2.2563.8441760
X-RAY DIFFRACTIONr_mcbond_other2.2543.8421759
X-RAY DIFFRACTIONr_mcangle_it3.3295.7492196
LS refinement shellResolution: 1.79→1.837 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 158 -
Rwork0.274 3175 -
all-3333 -
obs--99.85 %

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