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- PDB-3hzy: Crystal structure of S73-2 antibody in complex with antigen Kdo(2... -

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Basic information

Entry
Database: PDB / ID: 3hzy
TitleCrystal structure of S73-2 antibody in complex with antigen Kdo(2.4)Kdo(2.4)Kdo
Components(S73-2 Fab (IgG1k) ...) x 2
KeywordsIMMUNE SYSTEM / antibody / Fab / IgG / carbohydrate
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsBrooks, C.L. / Muller-Loennies, S. / Borisova, S.N. / Brade, L. / Kosma, P. / Hirama, T. / MacKenzie, C.R. / Brade, H. / Evans, S.V.
CitationJournal: Biochemistry / Year: 2010
Title: Antibodies raised against chlamydial lipopolysaccharide antigens reveal convergence in germline gene usage and differential epitope recognition
Authors: Brooks, C.L. / Muller-Loennies, S. / Borisova, S.N. / Brade, L. / Kosma, P. / Hirama, T. / Mackenzie, C.R. / Brade, H. / Evans, S.V.
History
DepositionJun 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Apr 8, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / struct_conn / struct_ref_seq / 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_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.type_symbol / _chem_comp.type / _struct_ref_seq.db_align_end
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_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_PDB_ins_code / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.pdbx_value_order / _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.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Sep 6, 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 3.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S73-2 Fab (IgG1k) light chain
B: S73-2 Fab (IgG1k) heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6719
Polymers48,6422
Non-polymers1,0297
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-22.7 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.945, 81.966, 128.242
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules AB

#1: Antibody S73-2 Fab (IgG1k) light chain


Mass: 24199.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c
#2: Antibody S73-2 Fab (IgG1k) heavy chain


Mass: 24442.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) / Strain: Balb/c

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Sugars , 1 types, 1 molecules

#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-(2-4)-prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2-ulopyranosidonic acid


Type: oligosaccharide / Mass: 718.610 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,3,2/[Aad1122h-2a_2-6_2*OCC=C][Aad1122h-2a_2-6]/1-2-2/a4-b2_b4-c2WURCSPDB2Glycan 1.1.0
[][propyl]{[(1+2)][a-D-Kdop]{[(4+2)][a-D-Kdop]{[(4+2)][a-D-Kdop]{}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 336 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 4000, Ethylene glycol, ZnCl2, MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002+ / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 26, 2007 / Details: Osmic Blue
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→19.8 Å / Num. obs: 28056 / % possible obs: 96.6 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.094 / Χ2: 0.78 / Scaling rejects: 12125
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.1-2.174.310.224.81326528000.9498.6
2.17-2.264.350.1935.21337028050.9298.7
2.26-2.364.360.1665.81346128170.8698.5
2.36-2.494.380.1416.61348328090.8398.3
2.49-2.644.450.1197.61362128130.7897.7
2.64-2.854.420.1018.41372128310.6897.6
2.85-3.134.430.0899.91362028000.6496.9
3.13-3.594.440.08811.31364827970.6295.7
3.59-4.514.410.08613.21357327860.7194.3
4.51-19.84.440.08613.81382827980.8190.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata scaling
PHASERphasing
PHENIX1.4_4refinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Q9R

1q9r
PDB Unreleased entry


Resolution: 2.1→19.8 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.816 / SU ML: 0.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.261 1989 7.13 %
Rwork0.216 --
obs0.219 27900 96.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.942 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso max: 71.62 Å2 / Biso mean: 32.236 Å2 / Biso min: 16.15 Å2
Baniso -1Baniso -2Baniso -3
1-5.073 Å2-0 Å20 Å2
2---4.818 Å20 Å2
3----0.255 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3342 0 55 330 3727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063476
X-RAY DIFFRACTIONf_angle_d0.9444729
X-RAY DIFFRACTIONf_chiral_restr0.065538
X-RAY DIFFRACTIONf_plane_restr0.004592
X-RAY DIFFRACTIONf_dihedral_angle_d16.8661241
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.1520.2871400.2161834197498
2.152-2.2110.2651450.2141857200298
2.211-2.2760.2871430.2171856199998
2.276-2.3490.2531430.221861200498
2.349-2.4330.2791450.2271864200998
2.433-2.530.2851400.2211840198097
2.53-2.6450.3141420.2311846198897
2.645-2.7840.3021430.2281864200797
2.784-2.9580.2831380.2281849198796
2.958-3.1850.3081420.2271839198196
3.185-3.5040.2391430.2141874201796
3.504-4.0080.2171410.1991836197795
4.008-5.0350.1921410.1761833197493
5.035-19.80.2531430.2041858200189

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