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- PDB-3ijs: Structure of S67-27 in Complex with TSBP -

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Basic information

Entry
Database: PDB / ID: 3ijs
TitleStructure of S67-27 in Complex with TSBP
Components
  • Immunoglobulin heavy chain (IGG3)
  • Immunoglobulin light chain (IGG3)
KeywordsIMMUNE SYSTEM / antibody / Kdo / Chlamydia / LPS / Fab / carbohydrate
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsBrooks, C.L. / Blackler, R.J. / Evans, S.V.
CitationJournal: Glycobiology / Year: 2010
Title: The role of CDR H3 in antibody recognition of a synthetic analog of a lipopolysaccharide antigen.
Authors: Brooks, C.L. / Blackler, R.J. / Sixta, G. / Kosma, P. / Muller-Loennies, S. / Brade, L. / Hirama, T. / Mackenzie, C.R. / Brade, H. / Evans, S.V.
History
DepositionAug 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_struct_conn_angle / pdbx_validate_chiral / 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_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunoglobulin light chain (IGG3)
B: Immunoglobulin heavy chain (IGG3)
C: Immunoglobulin light chain (IGG3)
D: Immunoglobulin heavy chain (IGG3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,8978
Polymers97,4494
Non-polymers1,4484
Water8,107450
1
A: Immunoglobulin light chain (IGG3)
B: Immunoglobulin heavy chain (IGG3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4484
Polymers48,7242
Non-polymers7242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-20 kcal/mol
Surface area19410 Å2
MethodPISA
2
C: Immunoglobulin light chain (IGG3)
D: Immunoglobulin heavy chain (IGG3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4484
Polymers48,7242
Non-polymers7242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-19 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.320, 127.910, 156.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Immunoglobulin light chain (IGG3)


Mass: 24193.826 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) / Strain: BALB/c
#2: Antibody Immunoglobulin heavy chain (IGG3)


Mass: 24530.635 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) / Strain: BALB/c
#3: Polysaccharide 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic ...3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 699.505 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[a2122h-1a_1-5_2*N_4*OPO/3O/3=O][Aad1122h-2a_2-6]/1-2-2/a6-b2_b4-c2WURCSPDB2Glycan 1.1.0
[][b-D-GlcpN]{[(4+0)][P]{}[(6+2)][a-D-Kdop]{[(4+2)][a-D-Kdop]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, MgCl2, pH 8.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 18, 2009 / Details: mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→19.93 Å / Num. obs: 30835 / % possible obs: 99 % / Redundancy: 3.59 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 8.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obs% possible all
2.55-2.643.680.273.699.2
2.64-2.753.650.2353.899.3
2.75-2.873.660.1934.599.3
2.87-3.023.660.1515.899.1
3.02-3.213.60.1197.199.1
3.21-3.463.610.091998.8
3.46-3.83.590.07410.898.8
3.8-4.353.50.05813.198.8
4.35-5.463.510.04815.798.3
5.46-19.933.50.051599.1

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Processing

Software
NameVersionClassificationNB
d*TREK9.7 W8RSSIdata processing
PHENIX1.4_4refinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3IJH

3ijh


Resolution: 2.55→19.929 Å / Occupancy max: 1 / Occupancy min: 0.28 / SU ML: 2.13 / σ(F): 0.03 / Phase error: 27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2605 1495 5.03 %
Rwork0.2166 --
obs0.2188 29719 95.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.176 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso mean: 30.419 Å2
Baniso -1Baniso -2Baniso -3
1-6.235 Å2-0 Å20 Å2
2---6.197 Å20 Å2
3----0.039 Å2
Refinement stepCycle: LAST / Resolution: 2.55→19.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6747 0 94 450 7291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037008
X-RAY DIFFRACTIONf_angle_d0.6429536
X-RAY DIFFRACTIONf_dihedral_angle_d15.8042499
X-RAY DIFFRACTIONf_chiral_restr0.0421085
X-RAY DIFFRACTIONf_plane_restr0.0031193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.63210.34621120.28932513X-RAY DIFFRACTION94
2.6321-2.7260.32431400.27372523X-RAY DIFFRACTION94
2.726-2.83480.36031350.27292442X-RAY DIFFRACTION95
2.8348-2.96350.30391420.25562517X-RAY DIFFRACTION95
2.9635-3.11920.29061440.24862528X-RAY DIFFRACTION95
3.1192-3.31380.29851270.23442560X-RAY DIFFRACTION95
3.3138-3.56830.23041410.2082535X-RAY DIFFRACTION95
3.5683-3.92490.22971380.19792556X-RAY DIFFRACTION96
3.9249-4.48720.2011370.16932618X-RAY DIFFRACTION96
4.4872-5.63210.21311390.15542644X-RAY DIFFRACTION96
5.6321-19.92930.21771400.18892788X-RAY DIFFRACTION97

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