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- PDB-4odu: Unliganded Fab structure of lipid A-specific antibody S1-15 -

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Basic information

Entry
Database: PDB / ID: 4odu
TitleUnliganded Fab structure of lipid A-specific antibody S1-15
Components
  • S1-15 Fab (IgG2b kappa) light chain
  • S1-15 Fab (IgG2b) heavy chain
KeywordsIMMUNE SYSTEM / Carbohydrate binding
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: 2.29 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 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Oct 7, 2015Group: Database references
Revision 1.3Nov 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 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 27, 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
L: S1-15 Fab (IgG2b kappa) light chain
H: S1-15 Fab (IgG2b) heavy chain
B: S1-15 Fab (IgG2b kappa) light chain
A: S1-15 Fab (IgG2b) heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3456
Polymers96,1534
Non-polymers1922
Water5,405300
1
L: S1-15 Fab (IgG2b kappa) light chain
H: S1-15 Fab (IgG2b) heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1723
Polymers48,0762
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-38 kcal/mol
Surface area19410 Å2
MethodPISA
2
B: S1-15 Fab (IgG2b kappa) light chain
A: S1-15 Fab (IgG2b) heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1723
Polymers48,0762
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-39 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.787, 77.638, 71.958
Angle α, β, γ (deg.)90.00, 96.83, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11L
21B
12H
22A

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010L1 - 212
2010B1 - 212
1020H0 - 223
2020A0 - 223

NCS ensembles :
ID
1
2

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Components

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


Mass: 23727.059 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c
#2: Antibody S1-15 Fab (IgG2b) heavy chain


Mass: 24349.254 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.18 Å3/Da / Density % sol: 43.61 %
Crystal growTemperature: 289 K / pH: 7
Details: 25% (w/v) PEG 2000 MME, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9794
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 1, 2011 / Details: VERTICAL FOCUSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.29→50 Å / Num. obs: 37458 / % possible obs: 100 % / Redundancy: 5 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 11.4
Reflection shellResolution: 2.29→2.34 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.615 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 43.68 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å29.4 Å
Translation2.5 Å29.4 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.14data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ODT

4odt


Resolution: 2.29→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 1 / SU B: 7.221 / SU ML: 0.175 / SU R Cruickshank DPI: 0.5229 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.523 / ESU R Free: 0.256 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1738 5 %RANDOM
Rwork0.187 ---
obs0.19 34731 92.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å2-0.25 Å2
2---0.08 Å2-0 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.29→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6662 0 10 300 6972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.026833
X-RAY DIFFRACTIONr_bond_other_d0.0040.026159
X-RAY DIFFRACTIONr_angle_refined_deg1.4181.9439305
X-RAY DIFFRACTIONr_angle_other_deg0.976314235
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5865861
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61224.029278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.596151083
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2841532
X-RAY DIFFRACTIONr_chiral_restr0.1020.21039
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217766
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021574
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_it1.9283.0733462
X-RAY DIFFRACTIONr_mcbond_other1.9263.0723461
X-RAY DIFFRACTIONr_mcangle_it3.2074.5974317
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
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11L109200.14
12B109200.14
21H112460.12
22A112460.12
LS refinement shellResolution: 2.29→2.35 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 61 -
Rwork0.214 1087 -
obs--41.7 %

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