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- PDB-6c5j: S25-23 Fab in complex with Chlamydiaceae LPS (Crystal form 1) -

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Basic information

Entry
Database: PDB / ID: 6c5j
TitleS25-23 Fab in complex with Chlamydiaceae LPS (Crystal form 1)
Components
  • IgG1 Fab Heavy Chain
  • IgG1 Fab Light Chain (Kappa)
KeywordsIMMUNE SYSTEM / SUGAR BINDING PROTEIN / Carbohydrate / Lipopolysaccharide / Antibody / Antigen / Complex / Chlamydia
Function / homology
Function and homology information


immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / immune response / extracellular space / extracellular exosome / metal ion binding
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
MAb 110 light chain / Igh protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsHaji-Ghassemi, O. / Evans, S.V.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)Discovery Grant 171356-2013 Canada
CitationJournal: Biochemistry / Year: 2019
Title: Subtle Changes in the Combining Site of the Chlamydiaceae-Specific mAb S25-23 Increase the Antibody-Carbohydrate Binding Affinity by an Order of Magnitude.
Authors: Haji-Ghassemi, O. / Muller-Loennies, S. / Brooks, C.L. / MacKenzie, C.R. / Caveney, N. / Van Petegem, F. / Brade, L. / Kosma, P. / Brade, H. / Evans, S.V.
History
DepositionJan 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / 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.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _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 2.1Oct 4, 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

Downloads & links

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Assembly

Deposited unit
H: IgG1 Fab Heavy Chain
L: IgG1 Fab Light Chain (Kappa)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0384
Polymers47,6562
Non-polymers1,3822
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-22 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.233, 45.453, 75.671
Angle α, β, γ (deg.)90.000, 105.310, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody IgG1 Fab Heavy Chain


Mass: 23475.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q99LC4
#2: Antibody IgG1 Fab Light Chain (Kappa)


Mass: 24180.895 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A0A0F7R5U8
#3: Polysaccharide 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-8)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic ...3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-8)-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-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1160.817 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/3,5,4/[a2122h-1a_1-5_1*OPO/3O/3=O_2*N][a2122h-1b_1-5_2*N_4*OPO/3O/3=O][Aad1122h-2a_2-6]/1-2-3-3-3/a6-b1_b6-c2_c4-d2_d8-e2WURCSPDB2Glycan 1.1.0
[][P]{[(0+1)][a-D-GlcpN]{[(6+1)][b-D-GlcpN]{[(4+0)][P]{}[(6+2)][a-D-Kdop]{[(4+2)][a-D-Kdop]{[(8+2)][a-D-Kdop]{}}}}}}LINUCSPDB-CARE
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.02 Å3/Da / Density % sol: 39.19 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M MES, 20% [w/v] polyethylene glycol [PEG] 10000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 5, 2014 / Details: DCM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.29→25 Å / Num. obs: 16502 / % possible obs: 93.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.069 / Χ2: 1.024 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.29-2.373.30.51917000.96196.7
2.37-2.473.30.42716650.99196.5
2.47-2.583.30.32116820.965196.9
2.58-2.713.40.21617111.011197.4
2.71-2.883.40.15416991.012197.5
2.88-3.113.40.10216631.067195
3.11-3.423.40.07116371.078193.9
3.42-3.913.40.05116170.999191
3.91-4.923.40.04115821189.5
4.92-253.50.05115461.165184.5

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M7J

4m7j


Resolution: 2.29→25 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.46 / SU ML: 0.2 / SU R Cruickshank DPI: 0.6504 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.65 / ESU R Free: 0.268
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2391 806 4.9 %RANDOM
Rwork0.1933 ---
obs0.1955 15554 93.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 124.78 Å2 / Biso mean: 53.065 Å2 / Biso min: 31.94 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å23.36 Å2
2---1.95 Å2-0 Å2
3---0.74 Å2
Refinement stepCycle: final / Resolution: 2.29→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3332 0 90 34 3456
Biso mean--66.7 48.65 -
Num. residues----435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.023515
X-RAY DIFFRACTIONr_bond_other_d0.0020.023103
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.9694808
X-RAY DIFFRACTIONr_angle_other_deg0.9233.0097259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3035433
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55424.167132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.26515540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4451513
X-RAY DIFFRACTIONr_chiral_restr0.0780.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213792
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02688
LS refinement shellResolution: 2.29→2.349 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 76 -
Rwork0.274 1126 -
all-1202 -
obs--96.39 %

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