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- PDB-4z8f: Fab structure of antibody S1-15 in complex with ssDNA DNA, 5'-p5(... -

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Basic information

Entry
Database: PDB / ID: 4z8f
TitleFab structure of antibody S1-15 in complex with ssDNA DNA, 5'-p5(dT)p-3'
Components
  • 5'-D(P*TP*TP*TP*TP*T)-3'
  • S1-15 Fab (IgG2b kappa) light chain
  • S1-15 Fab (IgG2b) heavy chain
KeywordsIMMUNE SYSTEM/DNA / antibody / Fab / carbohydrate / lipid A / DNA / IMMUNE SYSTEM-DNA complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DNA
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsHaji-Ghassemi, O. / Evans, S.V.
Funding support Austria, Canada, 2items
OrganizationGrant numberCountry
FWFP22909 Austria
Natural Sciences and Engineering Research Council (NSERC, Canada)OGP0171356 Canada
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 8, 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 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: S1-15 Fab (IgG2b) heavy chain
L: S1-15 Fab (IgG2b kappa) light chain
E: 5'-D(P*TP*TP*TP*TP*T)-3'
A: 5'-D(P*TP*TP*TP*TP*T)-3'


Theoretical massNumber of molelcules
Total (without water)51,2754
Polymers51,2754
Non-polymers00
Water3,531196
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.585, 77.585, 156.267
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 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 kappa) 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: DNA chain 5'-D(P*TP*TP*TP*TP*T)-3'


Mass: 1555.987 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.38 Å3/Da / Density % sol: 48.39 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.075M magnesium chloride, 0.1M HEPES pH 7.5, 28% (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: Dec 20, 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: 1.75→25 Å / Num. obs: 46712 / % possible obs: 99.9 % / Redundancy: 14.5 % / Rsym value: 0.059 / Net I/σ(I): 36
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 5.96 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.80073refinement
HKL-2000data collection
SCALAdata scaling
PHASER2.5.6phasing
PDB_EXTRACT3.15data extraction
HKL-2000v703c3data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ODT

4odt


Resolution: 1.75→25 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.91 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2438 5 %RANDOM
Rwork0.208 ---
obs0.209 46712 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.87 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å20 Å2
2--1.5 Å20 Å2
3----2.99 Å2
Refinement stepCycle: LAST / Resolution: 1.75→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3375 110 0 196 3681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193581
X-RAY DIFFRACTIONr_bond_other_d0.0010.023179
X-RAY DIFFRACTIONr_angle_refined_deg1.2841.9164896
X-RAY DIFFRACTIONr_angle_other_deg0.7837360
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4915439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.16224.113141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52115549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6551516
X-RAY DIFFRACTIONr_chiral_restr0.080.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213981
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02805
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_it2.1893.8451760
X-RAY DIFFRACTIONr_mcbond_other2.193.8431759
X-RAY DIFFRACTIONr_mcangle_it3.265.7562196
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: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 184 -
Rwork0.272 3315 -
obs--97.85 %

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