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- PDB-7oo2: Crystal structure of an antibody targeting the capsular polysacch... -

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Basic information

Entry
Database: PDB / ID: 7oo2
TitleCrystal structure of an antibody targeting the capsular polysaccharide of serogroup X Neisseria meningitidis (MenX)
Components
  • anti-MenX Fab heavy chain
  • anti-MenX Fab light chain
KeywordsANTIMICROBIAL PROTEIN / Antibody / Fragment antigen binding / Neisseria meningitidis / serogroup X / MenX / glycoconjugate vaccine
Function / homologyTHIOCYANATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.16 Å
AuthorsPietri, G.P. / de Ruyck, J. / Lenac, T. / Adamo, R. / Bouckaert, J.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
Marie Sklodowska-Curie Actions, FragNET ITN675671European Union
CitationJournal: Front Mol Biosci / Year: 2021
Title: Elucidating the Structural and Minimal Protective Epitope of the Serogroup X Meningococcal Capsular Polysaccharide.
Authors: Pietri, G.P. / Tontini, M. / Brogioni, B. / Oldrini, D. / Robakiewicz, S. / Henriques, P. / Calloni, I. / Abramova, V. / Santini, L. / Malic, S. / Miklic, K. / Lisnic, B. / Bertuzzi, S. / ...Authors: Pietri, G.P. / Tontini, M. / Brogioni, B. / Oldrini, D. / Robakiewicz, S. / Henriques, P. / Calloni, I. / Abramova, V. / Santini, L. / Malic, S. / Miklic, K. / Lisnic, B. / Bertuzzi, S. / Unione, L. / Balducci, E. / de Ruyck, J. / Romano, M.R. / Jimenez-Barbero, J. / Bouckaert, J. / Jonjic, S. / Rovis, T.L. / Adamo, R.
History
DepositionMay 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 10, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id ..._struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: anti-MenX Fab heavy chain
B: anti-MenX Fab light chain
C: anti-MenX Fab heavy chain
D: anti-MenX Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3157
Polymers96,1414
Non-polymers1743
Water7,404411
1
A: anti-MenX Fab heavy chain
B: anti-MenX Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1874
Polymers48,0712
Non-polymers1162
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: anti-MenX Fab heavy chain
D: anti-MenX Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1293
Polymers48,0712
Non-polymers581
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.012, 85.349, 123.272
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "C"
d_1ens_2(chain "B" and (resid 1 through 186 or resid 188 through 214))
d_2ens_2(chain "D" and (resid 1 through 186 or resid 188 through 214))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLNGLNTHRTHRAA1 - 2181 - 218
d_21ens_1GLNGLNTHRTHRCC1 - 2181 - 218
d_11ens_2GLUGLUTYRTYRBB1 - 1861 - 186
d_12ens_2ARGARGCYSCYSBB188 - 214188 - 214
d_21ens_2GLUGLUTYRTYRDD1 - 1861 - 186
d_22ens_2ARGARGCYSCYSDD188 - 214188 - 214

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.867168948608, -0.490265725447, -0.087507331251), (-0.483965396713, 0.871036386498, -0.0841017727555), (0.117454286236, -0.0305799255723, -0.992607353789)13.0225533232, 1.94583808463, -65.4120739771
2given(-0.875739393393, -0.476238727864, -0.0792287128668), (-0.471447215347, 0.878935832541, -0.07217565668), (0.104009797625, -0.0258549097421, -0.994240154912)13.4254416833, 1.77747845393, -65.0286486531

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Components

#1: Antibody anti-MenX Fab heavy chain


Mass: 24436.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fragment antigen-binding from mouse, heavy chain, with CH1 matching the IgG2 mouse heavy chain sequences.
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Hek293T / Production host: Homo sapiens (human)
#2: Antibody anti-MenX Fab light chain


Mass: 23633.994 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Fragment antigen-binding from mouse, light chain, with CL matching the IgG2 mouse light chain sequences.
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Hek293FS / Production host: Homo sapiens (human)
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 44.1 % / Description: diamond
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M potassium thiocyanate 0.1 M Bis-Tris propane at pH 6.5 20% PEG 3350 (F4 < PACT Premier HT screen Molecular Dimensions)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.16→50 Å / Num. obs: 47671 / % possible obs: 99.93 % / Observed criterion σ(I): -3 / Redundancy: 13.6 % / Biso Wilson estimate: 55.42 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.066 / Net I/σ(I): 23.09
Reflection shellResolution: 2.16→2.29 Å / Redundancy: 13.7 % / Rmerge(I) obs: 1.174 / Mean I/σ(I) obs: 1.99 / Num. unique obs: 7559 / CC1/2: 0.755 / Rrim(I) all: 1.219 / Rsym value: 1.31 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4m1g

4m1g


Resolution: 2.16→49.49 Å / SU ML: 0.3751 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1598
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2623 1995 4.18 %Random selection
Rwork0.213 45697 --
obs0.215 47665 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.37 Å2
Refinement stepCycle: LAST / Resolution: 2.16→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6582 0 9 411 7002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00356751
X-RAY DIFFRACTIONf_angle_d0.71439202
X-RAY DIFFRACTIONf_chiral_restr0.04651053
X-RAY DIFFRACTIONf_plane_restr0.00421172
X-RAY DIFFRACTIONf_dihedral_angle_d12.59682419
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.48139254405
ens_2d_2BX-RAY DIFFRACTIONTorsion NCS0.832655414471
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.210.40241390.38293141X-RAY DIFFRACTION97.79
2.21-2.270.3631430.3463226X-RAY DIFFRACTION100
2.27-2.340.35961360.3133236X-RAY DIFFRACTION100
2.34-2.410.35361430.31043229X-RAY DIFFRACTION99.97
2.42-2.50.36881360.32253229X-RAY DIFFRACTION100
2.5-2.60.40291430.33213260X-RAY DIFFRACTION100
2.6-2.720.3771430.30593223X-RAY DIFFRACTION100
2.72-2.860.30981420.29353257X-RAY DIFFRACTION99.97
2.86-3.040.30781470.26243229X-RAY DIFFRACTION99.97
3.04-3.280.31431400.25683271X-RAY DIFFRACTION100
3.28-3.610.27571460.20133288X-RAY DIFFRACTION100
3.61-4.130.2281390.17073309X-RAY DIFFRACTION100
4.13-5.20.17251450.13623326X-RAY DIFFRACTION100
5.2-49.490.22941530.18533473X-RAY DIFFRACTION99.86

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