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- PDB-3bpc: co-crystal structure of S25-2 Fab in complex with 5-deoxy-4-epi-2... -

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Basic information

Entry
Database: PDB / ID: 3bpc
Titleco-crystal structure of S25-2 Fab in complex with 5-deoxy-4-epi-2,3-dehydro Kdo (4.8) Kdo
Components(Fab, antibody fragment (IgG1k), ...) x 2
KeywordsIMMUNE SYSTEM / Fab / anti-carbohydrate antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsBrooks, C.L. / Evans, S.V.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Exploration of specificity in germline monoclonal antibody recognition of a range of natural and synthetic epitopes.
Authors: Brooks, C.L. / Muller-Loennies, S. / Brade, L. / Kosma, P. / Hirama, T. / MacKenzie, C.R. / Brade, H. / Evans, S.V.
History
DepositionDec 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 2.0Jun 24, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_src_nat / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_conn / struct_ref / struct_ref_seq
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.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _entity_src_nat.pdbx_ncbi_taxonomy_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_asym_id
Revision 3.0Jul 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_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 / 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 / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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
A: Fab, antibody fragment (IgG1k), light chain
B: Fab, antibody fragment (IgG1k), heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9987
Polymers48,3542
Non-polymers6445
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-61 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.850, 81.290, 132.340
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 Fab, antibody fragment (IgG1k), light chain


Mass: 24242.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse)
#2: Antibody Fab, antibody fragment (IgG1k), heavy chain


Mass: 24110.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse)

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Sugars , 1 types, 1 molecules

#3: Polysaccharide 3,4,5-trideoxy-alpha-D-erythro-oct-3-en-2-ulopyranosonic acid-(2-8)-prop-2-en-1-yl 3-deoxy-alpha-D- ...3,4,5-trideoxy-alpha-D-erythro-oct-3-en-2-ulopyranosonic acid-(2-8)-prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2-ulopyranosidonic acid


Type: oligosaccharide / Mass: 464.418 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][Aazzd22h-2a_2-6]/1-2/a8-b2WURCSPDB2Glycan 1.1.0
[][propyl]{[(1+2)][a-D-Kdop]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 465 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 461 / 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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growMethod: vapor diffusion / pH: 8
Details: PEG 4000, ethelyene glycol, pH 8.0, VAPOR DIFFUSION

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 7, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→19.97 Å / Num. obs: 44150 / % possible obs: 94.5 % / Redundancy: 3.49 % / Rmerge(I) obs: 0.073 / Χ2: 0.96 / Net I/σ(I): 9 / Scaling rejects: 2609
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.8-1.863.730.22841715545500.8799.5
1.86-1.943.860.2174.11793945970.9399.2
1.94-2.033.830.1585.51755945330.8698.5
2.03-2.133.760.1386.61721045200.997.9
2.13-2.273.870.1546.61764644960.9997.3
2.27-2.443.480.1057.91565644420.9495.7
2.44-2.693.080.08110.11344542960.9492
2.69-3.072.90.06712.21244142120.9689.9
3.07-3.873.080.05815.21334042391.0289.4
3.87-19.973.20.049241435042651.386.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.97 Å
Translation2.5 Å19.97 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.912 / SU B: 3.678 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.273 2071 5.1 %RANDOM
Rwork0.224 ---
obs0.226 40510 94.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.304 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å20 Å20 Å2
2---0.8 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3315 0 36 461 3812
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223431
X-RAY DIFFRACTIONr_angle_refined_deg1.7231.9654673
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.125426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.1523.806134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20815547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4311516
X-RAY DIFFRACTIONr_chiral_restr0.1230.2527
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022566
X-RAY DIFFRACTIONr_nbd_refined0.2220.21639
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22300
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2840.2390
X-RAY DIFFRACTIONr_metal_ion_refined0.0950.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.222
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.4280.27
X-RAY DIFFRACTIONr_mcbond_it1.0021.52197
X-RAY DIFFRACTIONr_mcangle_it1.57123473
X-RAY DIFFRACTIONr_scbond_it2.62931442
X-RAY DIFFRACTIONr_scangle_it3.6564.51200
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 172 -
Rwork0.37 2922 -
all-3094 -
obs--99.33 %

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