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

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Basic information

Entry
Database: PDB / ID: 3hzk
TitleCrystal structure of S73-2 antibody in complex with antigen 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: 2.15 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 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_conn_type / 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_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.conn_type_id / _struct_conn.id / _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.ptnr1_label_seq_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 / _struct_conn_type.id / _struct_ref_seq.db_align_end
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 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

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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)49,2756
Polymers48,6622
Non-polymers6124
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-22.6 kcal/mol
Surface area19870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.340, 80.940, 128.160
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: 24213.967 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: 24448.295 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)-prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2- ...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: 498.433 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[Aad1122h-2a_2-6_2*OCC=C][Aad1122h-2a_2-6]/1-2/a4-b2WURCSPDB2Glycan 1.1.0
[][propyl]{[(1+2)][a-D-Kdop]{[(4+2)][a-D-Kdop]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 169 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.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.47 Å3/Da / Density % sol: 50.19 %
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 24, 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: 2.15→19.86 Å / Num. obs: 25575 / % possible obs: 94.9 % / Redundancy: 4.73 % / Rmerge(I) obs: 0.061 / Χ2: 0.99 / Scaling rejects: 915
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.15-2.234.660.2963.81224826241.1998.2
2.23-2.324.730.26341224825851.1597.5
2.32-2.424.750.2234.61215725551.1297.2
2.42-2.554.80.1915.31232725651.0896.2
2.55-2.714.830.1456.71236525531.0295.6
2.71-2.924.870.1078.81247025520.9895.2
2.92-3.214.860.07613.41237125231.0394.5
3.21-3.674.770.05119.41224925300.8493.3
3.67-4.614.480.03724.31164125510.7393
4.61-19.864.590.03427.41190925370.7188.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 32.89 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.75 Å
Translation2.5 Å19.75 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata scaling
PHASER2.1.1phasing
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: 2.15→19.752 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.778 / SU ML: 0.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.26 1294 5.06 %
Rwork0.214 --
obs0.217 25568 94.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.193 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso max: 81.78 Å2 / Biso mean: 34.031 Å2 / Biso min: 17.42 Å2
Baniso -1Baniso -2Baniso -3
1--0.081 Å20 Å2-0 Å2
2--0.157 Å2-0 Å2
3----0.075 Å2
Refinement stepCycle: LAST / Resolution: 2.15→19.752 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3387 0 37 166 3590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063505
X-RAY DIFFRACTIONf_angle_d1.0654764
X-RAY DIFFRACTIONf_chiral_restr0.074538
X-RAY DIFFRACTIONf_plane_restr0.004600
X-RAY DIFFRACTIONf_dihedral_angle_d18.011249
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.15-2.2360.3121190.2352782290198
2.236-2.3380.3191250.242745287097
2.338-2.4610.3521410.2392707284897
2.461-2.6150.3461320.2462699283196
2.615-2.8160.3151520.2422685283796
2.816-3.0980.2831540.2442686284095
3.098-3.5450.2681690.2162623279294
3.545-4.4570.2071410.1752681282293
4.457-19.7520.1751610.162666282789

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