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- PDB-8doz: Protective antibody against gonococcal lipooligosaccharide -

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Basic information

Entry
Database: PDB / ID: 8doz
TitleProtective antibody against gonococcal lipooligosaccharide
Components
  • Fab 2C7 lambda light chain
  • Fab 2C7, heavy chain Fd fragment
KeywordsIMMUNE SYSTEM / Antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBeernink, P.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI134868 United States
CitationJournal: Jacs Au / Year: 2024
Title: Gonococcal Mimitope Vaccine Candidate Forms a Beta-Hairpin Turn and Binds Hydrophobically to a Therapeutic Monoclonal Antibody.
Authors: Beernink, P.T. / Di Carluccio, C. / Marchetti, R. / Cerofolini, L. / Carillo, S. / Cangiano, A. / Cowieson, N. / Bones, J. / Molinaro, A. / Paduano, L. / Fragai, M. / Beernink, B.P. / ...Authors: Beernink, P.T. / Di Carluccio, C. / Marchetti, R. / Cerofolini, L. / Carillo, S. / Cangiano, A. / Cowieson, N. / Bones, J. / Molinaro, A. / Paduano, L. / Fragai, M. / Beernink, B.P. / Gulati, S. / Shaughnessy, J. / Rice, P.A. / Ram, S. / Silipo, A.
History
DepositionJul 14, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.3Nov 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab 2C7, heavy chain Fd fragment
B: Fab 2C7 lambda light chain
C: Fab 2C7, heavy chain Fd fragment
D: Fab 2C7 lambda light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,5688
Polymers93,2624
Non-polymers3064
Water9,692538
1
A: Fab 2C7, heavy chain Fd fragment
B: Fab 2C7 lambda light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9376
Polymers46,6312
Non-polymers3064
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-39 kcal/mol
Surface area19330 Å2
MethodPISA
2
C: Fab 2C7, heavy chain Fd fragment
D: Fab 2C7 lambda light chain


Theoretical massNumber of molelcules
Total (without water)46,6312
Polymers46,6312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-22 kcal/mol
Surface area19280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.000, 50.610, 106.210
Angle α, β, γ (deg.)92.130, 86.780, 82.260
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody Fab 2C7, heavy chain Fd fragment


Mass: 23786.412 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Recombinant chimeric Fab fragment (mouse/human) / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab 2C7 lambda light chain


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

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Non-polymers , 4 types, 542 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 538 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.085 M Na HEPES, 8.5% (v/v) 2-propanol, 17 % (w/v) PEG 4,000, 15% (v/v) 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 PILATUS3 6M / Detector: PIXEL / Date: Mar 31, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11 Å / Relative weight: 1
ReflectionResolution: 1.7→106.14 Å / Num. obs: 294917 / % possible obs: 91.6 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 24.47 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.027 / Rrim(I) all: 0.052 / Net I/σ(I): 19.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.859 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 26592 / CC1/2: 0.789 / Rpim(I) all: 0.027 / Rrim(I) all: 0.997 / % possible all: 83.8

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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: 6rco (homology model)

6rco


Resolution: 1.7→52.97 Å / SU ML: 0.1852 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 24.9166
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2159 1324 1.61 %
Rwork0.1772 80930 -
obs0.1778 82254 90.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→52.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6328 0 19 538 6885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01046526
X-RAY DIFFRACTIONf_angle_d1.13948923
X-RAY DIFFRACTIONf_chiral_restr0.0641025
X-RAY DIFFRACTIONf_plane_restr0.01291131
X-RAY DIFFRACTIONf_dihedral_angle_d14.45462280
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.770.28221340.25188259X-RAY DIFFRACTION83.4
1.77-1.850.31911330.25748447X-RAY DIFFRACTION85.2
1.85-1.950.26171470.21038800X-RAY DIFFRACTION88.79
1.95-2.070.24161530.18958937X-RAY DIFFRACTION90.4
2.07-2.230.23351440.18899227X-RAY DIFFRACTION92.54
2.23-2.450.25131550.18739201X-RAY DIFFRACTION93.51
2.45-2.810.20761530.18539370X-RAY DIFFRACTION94.52
2.81-3.540.23541530.17159340X-RAY DIFFRACTION94.5
3.54-52.970.16861520.15269349X-RAY DIFFRACTION94.22
Refinement TLS params.Method: refined / Origin x: -23.3886582428 Å / Origin y: 19.4595794538 Å / Origin z: -47.1477009845 Å
111213212223313233
T0.220009717524 Å2-0.0109354822178 Å25.62526078791E-5 Å2-0.173457643483 Å20.00812613516112 Å2--0.200130443612 Å2
L0.0781590570698 °2-0.0263968303279 °20.0184530739756 °2--0.0523728469698 °20.0435181954068 °2--0.142662434519 °2
S0.0161546238101 Å °0.0202460145191 Å °0.0103212991374 Å °-0.00226114196093 Å °-0.0171065832888 Å °0.0150880565579 Å °-0.0371544870952 Å °0.0131570469429 Å °2.75866184518E-6 Å °
Refinement TLS groupSelection details: all

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