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- PDB-4odv: Fab Structure of lipid A-specific antibody A6 in complex with lip... -

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Basic information

Entry
Database: PDB / ID: 4odv
TitleFab Structure of lipid A-specific antibody A6 in complex with lipid A carbohydrate backbone
Components
  • A6 Fab (IgG2b kappa) light chain
  • A6 Fab (IgG2b) heavy chain
KeywordsIMMUNE SYSTEM / Carbohydrate binding
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 16, 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: A6 Fab (IgG2b kappa) light chain
H: A6 Fab (IgG2b) heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2504
Polymers47,6442
Non-polymers6062
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-18 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.563, 64.285, 154.157
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody A6 Fab (IgG2b kappa) light chain


Mass: 23851.348 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c
#2: Antibody A6 Fab (IgG2b) heavy chain


Mass: 23792.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c
#3: Polysaccharide 2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 500.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5_1*OPO/3O/3=O_2*N][a2122h-1b_1-5_2*N_4*OPO/3O/3=O]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][P]{[(0+1)][a-D-GlcpN]{[(6+1)][b-D-GlcpN]{[(4+0)][P]{}}}}LINUCSPDB-CARE
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 1.95 Å3/Da / Density % sol: 37.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 25% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9794 Å
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: 2.15→25 Å / Num. obs: 21071 / % possible obs: 99.7 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.085 / Χ2: 1.064 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.15-2.234.50.40420560.989199.1
2.23-2.324.80.33120581.086199.7
2.32-2.4250.28620491.082199.9
2.42-2.555.20.23620881.0881100
2.55-2.715.30.18120771.0811100
2.71-2.925.20.13321101.0451100
2.92-3.215.10.10320911.098199.8
3.21-3.674.90.07821111.06199.8
3.67-4.624.60.06721611.005199.6
4.62-254.40.06122701.094199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å24.82 Å
Translation2.5 Å24.82 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.14data extraction
MacromolecularCrystallography Data Collector software (MxDC)data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ODT

4odt


Resolution: 2.15→24.83 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.2785 / WRfactor Rwork: 0.2213 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8231 / SU B: 6.355 / SU ML: 0.164 / SU R Cruickshank DPI: 0.3422 / SU Rfree: 0.2281 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.342 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 1073 5.1 %RANDOM
Rwork0.2044 ---
obs0.2067 21015 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.04 Å2 / Biso mean: 48.6741 Å2 / Biso min: 24.71 Å2
Baniso -1Baniso -2Baniso -3
1-3.66 Å2-0 Å2-0 Å2
2---1.59 Å20 Å2
3----2.07 Å2
Refinement stepCycle: LAST / Resolution: 2.15→24.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3338 0 38 94 3470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023480
X-RAY DIFFRACTIONr_bond_other_d0.0020.023169
X-RAY DIFFRACTIONr_angle_refined_deg1.5641.9734745
X-RAY DIFFRACTIONr_angle_other_deg0.8053.0037318
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0955440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.50623.969131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.10915559
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0031515
X-RAY DIFFRACTIONr_chiral_restr0.0940.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213887
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02764
X-RAY DIFFRACTIONr_mcbond_it3.2034.7091760
X-RAY DIFFRACTIONr_mcbond_other3.2044.7081759
X-RAY DIFFRACTIONr_mcangle_it4.8537.0462200
LS refinement shellResolution: 2.151→2.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 91 -
Rwork0.247 1432 -
all-1523 -
obs--98.51 %

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