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- PDB-4c83: Crystal Structure of the IgG2a LPT3 in complex with an 8-sugar in... -

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Basic information

Entry
Database: PDB / ID: 4c83
TitleCrystal Structure of the IgG2a LPT3 in complex with an 8-sugar inner core analogue of Neisseria meningitidis
Components
  • LPT3 HEAVY CHAIN
  • LPT3 LIGHT CHAIN
KeywordsIMMUNE SYSTEM / LIPOOLIGOSACCHARIDES / ANTIBODIES / ANTIGEN-ANTIBODY COMPLEX
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsParker, M.J. / Gomery, K. / Richard, G. / Mackenzie, C.R. / Cox, A.D. / Richards, J.C. / Evans, S.V.
CitationJournal: Glycobiology / Year: 2014
Title: Structural Basis for Selective Cross-Reactivity in a Bactericidal Antibody Against Inner Core Lipooligosaccharide from Neisseria Meningitidis.
Authors: Parker, M.J. / Gomery, K. / Richard, G. / Mackenzie, C.R. / Cox, A.D. / Richards, J.C. / Evans, S.V.
History
DepositionSep 29, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2014Group: Database references
Revision 1.2Sep 23, 2015Group: Data collection
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LPT3 HEAVY CHAIN
B: LPT3 LIGHT CHAIN
C: LPT3 HEAVY CHAIN
D: LPT3 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,5178
Polymers94,3494
Non-polymers2,1684
Water724
1
C: LPT3 HEAVY CHAIN
D: LPT3 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2584
Polymers47,1752
Non-polymers1,0842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-31.8 kcal/mol
Surface area19460 Å2
MethodPISA
2
A: LPT3 HEAVY CHAIN
B: LPT3 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2584
Polymers47,1752
Non-polymers1,0842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-29.8 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.628, 64.192, 64.403
Angle α, β, γ (deg.)87.51, 89.82, 73.41
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody LPT3 HEAVY CHAIN


Mass: 23656.555 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse)
#2: Antibody LPT3 LIGHT CHAIN


Mass: 23518.004 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse)
#3: Polysaccharide 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-L-glycero-alpha-D-manno-heptopyranose-(1-3)-[beta-D- ...2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-L-glycero-alpha-D-manno-heptopyranose-(1-3)-[beta-D-glucopyranose-(1-4)]L-glycero-alpha-D-manno-heptopyranose-(1-5)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid


Type: oligosaccharide / Mass: 987.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAca1-2LDmanHep1-3[DGlcpb1-4]LDmanHep1-5DKdopa2-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[Aad1122h-2a_2-6][a11221h-1a_1-5][a2122h-1a_1-5_2*NCC/3=O][a2122h-1b_1-5]/1-2-2-3-4/a5-b1_b3-c1_b4-e1_c2-d1WURCSPDB2Glycan 1.1.0
[][a-D-Kdop]{[(5+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-GlcpNAc]{}}[(4+1)][b-D-Glcp]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE NOT AVAILABLE ON DATABASES

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.22 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.69→40 Å / Num. obs: 26006 / % possible obs: 97.5 % / Observed criterion σ(I): 2 / Redundancy: 1.96 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.3
Reflection shellResolution: 2.69→2.79 Å / Redundancy: 1.95 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 3.3 / % possible all: 98.1

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MF2

1mf2


Resolution: 2.69→37.9 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.886 / SU B: 17.607 / SU ML: 0.357 / Cross valid method: THROUGHOUT / ESU R Free: 0.421 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT.
RfactorNum. reflection% reflectionSelection details
Rfree0.29255 1319 5.1 %RANDOM
Rwork0.22484 ---
obs0.22845 24686 97.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.986 Å2
Baniso -1Baniso -2Baniso -3
1--1.94 Å2-0.24 Å22.31 Å2
2---1.51 Å20.4 Å2
3---3.63 Å2
Refinement stepCycle: LAST / Resolution: 2.69→37.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6543 0 144 4 6691
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.026859
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.9699326
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9545837
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.04323.385257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.611151062
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0271534
X-RAY DIFFRACTIONr_chiral_restr0.180.21061
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215020
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
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
LS refinement shellResolution: 2.69→2.76 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.447 77 -
Rwork0.356 1870 -
obs--98.09 %

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