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- PDB-8duz: Protective antibody against gonococcal lipooligosaccharide bound ... -

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Basic information

Entry
Database: PDB / ID: 8duz
TitleProtective antibody against gonococcal lipooligosaccharide bound to peptide mimetic
Components
  • Ig, lambda light chain
  • IgG heavy chain, Fd fragment
  • Mimetic peptide
KeywordsIMMUNE SYSTEM / Antibody / IMMUNE SYSTEM Peptide antigen
Function / homologyACETATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
Bacteriophage sp. (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBeernink, P.T. / Beernink, B.P. / Rice, P.A. / Ram, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI134868 United States
CitationJournal: to be published
Title: Protective antibody against gonococcal lipooligosaccharide bound to peptide mimetic
Authors: Beernink, P.T. / Beernink, B.P. / Ram, S.
History
DepositionJul 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IgG heavy chain, Fd fragment
C: IgG heavy chain, Fd fragment
D: Ig, lambda light chain
B: Ig, lambda light chain
E: Mimetic peptide
F: Mimetic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,13413
Polymers96,6826
Non-polymers4537
Water10,413578
1
A: IgG heavy chain, Fd fragment
B: Ig, lambda light chain
F: Mimetic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5177
Polymers48,3413
Non-polymers1774
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-45 kcal/mol
Surface area19220 Å2
MethodPISA
2
C: IgG heavy chain, Fd fragment
D: Ig, lambda light chain
E: Mimetic peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6176
Polymers48,3413
Non-polymers2763
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-31 kcal/mol
Surface area19050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.610, 64.190, 110.810
Angle α, β, γ (deg.)90.000, 97.120, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein/peptide , 1 types, 2 molecules EF

#3: Protein/peptide Mimetic peptide


Mass: 1695.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Bacteriophage sp. (virus)

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Antibody , 2 types, 4 molecules ACDB

#1: Antibody IgG heavy chain, Fd fragment


Mass: 23800.439 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Ig, lambda light chain


Mass: 22844.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 5 types, 585 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.14 Å3/Da / Density % sol: 42.51 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.17 M sodium acetate trihydrate 0.085 TrisHCl 22.5% PEG 4000 15% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 1.65→58.19 Å / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Biso Wilson estimate: 25.24 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.036 / Rrim(I) all: 0.094 / Net I/σ(I): 11.1
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.841 / Mean I/σ(I) obs: 1 / Num. unique obs: 64843 / CC1/2: 0.461 / Rpim(I) all: 0.766 / Rrim(I) all: 1.997 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8DOZ

8doz


Resolution: 1.65→58.16 Å / SU ML: 0.2328 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2637
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2339 1894 1.94 %
Rwork0.1892 95834 -
obs0.1901 97728 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.67 Å2
Refinement stepCycle: LAST / Resolution: 1.65→58.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6521 0 28 578 7127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01046764
X-RAY DIFFRACTIONf_angle_d1.06489256
X-RAY DIFFRACTIONf_chiral_restr0.0631066
X-RAY DIFFRACTIONf_plane_restr0.00981175
X-RAY DIFFRACTIONf_dihedral_angle_d14.4682378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.33841350.33076784X-RAY DIFFRACTION99.35
1.69-1.740.32591350.31996845X-RAY DIFFRACTION99.39
1.74-1.790.37251330.29736768X-RAY DIFFRACTION99.25
1.79-1.850.31791350.27186808X-RAY DIFFRACTION99.24
1.85-1.910.27651340.23296783X-RAY DIFFRACTION99.33
1.91-1.990.28691350.2166819X-RAY DIFFRACTION99.36
1.99-2.080.25061350.20366840X-RAY DIFFRACTION99.59
2.08-2.190.30931350.20276839X-RAY DIFFRACTION99.61
2.19-2.330.2531350.18466827X-RAY DIFFRACTION99.49
2.33-2.510.2451350.18516836X-RAY DIFFRACTION99.63
2.51-2.760.23991360.1876884X-RAY DIFFRACTION99.56
2.76-3.160.24661350.17866859X-RAY DIFFRACTION99.39
3.16-3.980.17631370.16266932X-RAY DIFFRACTION99.45
3.98-58.160.19831390.16677010X-RAY DIFFRACTION99.42
Refinement TLS params.Method: refined / Origin x: 1.0638202342 Å / Origin y: -22.6923414578 Å / Origin z: 27.625904359 Å
111213212223313233
T0.12497908157 Å20.00535331158129 Å2-0.000842472734812 Å2-0.135047392567 Å2-0.0246444779035 Å2--0.127448926652 Å2
L0.00622919005317 °20.020371802788 °2-0.0152171343932 °2-0.0113936763765 °20.0178440664518 °2--0.0133176997499 °2
S0.00255960519363 Å °-0.0130640884909 Å °0.00792612324497 Å °0.0152570439251 Å °-0.00451184891401 Å °-0.000420952336941 Å °-0.00259241647818 Å °0.0167029742474 Å °-1.00844549004E-13 Å °
Refinement TLS groupSelection details: all

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