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- PDB-6c5k: S25-23 Fab in complex with Chlamydiaceae LPS (Crystal form 2) -

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Basic information

Entry
Database: PDB / ID: 6c5k
TitleS25-23 Fab in complex with Chlamydiaceae LPS (Crystal form 2)
Components
  • IgG1 Fab Heavy Chain
  • IgG1 Fab Light Chain (Kappa)
KeywordsSUGAR BINDING PROTEIN / Carbohydrate / Lipopolysaccharide / Antibody / Antigen / Complex / Chlamydia
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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
NITRATE ION / MAb 110 light chain / Igh protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 2.0Jan 8, 2020Group: Author supporting evidence / Data collection / Polymer sequence
Category: chem_comp / entity_poly / pdbx_audit_support
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_audit_support.funding_organization
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / 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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 3.1Oct 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
A: IgG1 Fab Heavy Chain
L: IgG1 Fab Light Chain (Kappa)
B: IgG1 Fab Light Chain (Kappa)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,8019
Polymers95,2774
Non-polymers3,5255
Water16,376909
1
H: IgG1 Fab Heavy Chain
L: IgG1 Fab Light Chain (Kappa)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3704
Polymers47,6382
Non-polymers1,7312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-15 kcal/mol
Surface area20040 Å2
MethodPISA
2
A: IgG1 Fab Heavy Chain
B: IgG1 Fab Light Chain (Kappa)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4325
Polymers47,6382
Non-polymers1,7933
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-17 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.649, 62.710, 107.071
Angle α, β, γ (deg.)90.00, 116.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Antibody , 2 types, 4 molecules HALB

#1: Antibody IgG1 Fab Heavy Chain


Mass: 23457.441 Da / Num. of mol.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A0A0F7R5U8

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Sugars , 2 types, 4 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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.: 2
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

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Non-polymers , 2 types, 910 molecules

#5: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 909 / 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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium nitrate, 20% [w/v] polyethylene glycol 3350
PH range: 7.0-7.5

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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: 1.75→25 Å / Num. obs: 103537 / % possible obs: 99.9 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 14
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.619 / Num. unique obs: 7032 / % possible all: 100

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Processing

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

4m7j


Resolution: 1.75→25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.64 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.115 / ESU R Free: 0.109 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
RfactorNum. reflection% reflectionSelection details
Rfree0.218 5326 5.1 %RANDOM
Rwork0.188 ---
obs0.19 98210 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.91 Å2
Baniso -1Baniso -2Baniso -3
1--1.08 Å20 Å2-1.1 Å2
2--3.24 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.75→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6690 0 232 909 7831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.027126
X-RAY DIFFRACTIONr_bond_other_d0.0030.026455
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.9779748
X-RAY DIFFRACTIONr_angle_other_deg0.9983.00914982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1875869
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91424.151265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.38151091
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4971526
X-RAY DIFFRACTIONr_chiral_restr0.110.21149
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217766
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021560
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: 1.75→1.79 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 382 -
Rwork0.275 7032 -
obs--97.53 %

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