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- PDB-2r1w: Crystal structure of S25-2 Fab in complex with Kdo analogues -

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Basic information

Entry
Database: PDB / ID: 2r1w
TitleCrystal structure of S25-2 Fab in complex with Kdo analogues
Components(Fab, antibody fragment (IgG1k), ...Fragment antigen-binding) x 2
KeywordsIMMUNE SYSTEM / Fab / anti-carbohydrate antibody / Immunoglobulin C region / Immunoglobulin domain / Immunoglobulin V region / Secreted
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / immune response / extracellular space / metal ion binding
Similarity search - Function
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
VH coding region / ENSMUSG00000076577 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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
DepositionAug 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: 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 2.0Jul 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_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_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 / _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.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.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_type.id / _struct_ref_seq.db_align_end
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 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: Fab, antibody fragment (IgG1k), light chain
B: Fab, antibody fragment (IgG1k), heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0228
Polymers48,3542
Non-polymers6686
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-53 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.680, 81.200, 131.950
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 / Fragment antigen-binding


Mass: 24242.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q52L64*PLUS
#2: Antibody Fab, antibody fragment (IgG1k), heavy chain / Fragment antigen-binding


Mass: 24110.967 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascites / Source: (natural) Mus musculus (house mouse) / References: UniProt: A2NU21*PLUS

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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, 305 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.53 Å3/Da / Density % sol: 51.39 %
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-002 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→19.91 Å / Num. obs: 51889 / % possible obs: 94.6 % / Redundancy: 3.42 % / Rmerge(I) obs: 0.05 / Χ2: 1 / Net I/σ(I): 11.8 / Scaling rejects: 1343
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.7-1.763.030.2953.31571251611.1895.4
1.76-1.833.180.253.71646451441.1395.3
1.83-1.913.40.2034.61758951371.1194.9
1.91-2.023.460.1535.81782151251.0694.8
2.02-2.143.480.1217.21805151571.0194.9
2.14-2.313.550.09891871952230.9495.6
2.31-2.543.570.07811.21883252420.995.6
2.54-2.93.570.05416.21886852370.8695.4
2.9-3.663.570.0422.91883652380.994.5
3.66-19.913.40.03231.41806952250.9990.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.91 Å
Translation2.5 Å19.91 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3data extraction
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q9Q

1q9q
PDB Unreleased entry


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.266 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2650 5.1 %RANDOM
Rwork0.219 ---
obs0.221 51873 94.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.495 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å20 Å2
2---0.48 Å20 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3357 0 37 300 3694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223473
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.9624729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6715432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.70423.796137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6515553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4281517
X-RAY DIFFRACTIONr_chiral_restr0.1070.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022599
X-RAY DIFFRACTIONr_nbd_refined0.2130.21570
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22356
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2258
X-RAY DIFFRACTIONr_metal_ion_refined0.0820.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.217
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.3380.24
X-RAY DIFFRACTIONr_mcbond_it0.8761.52230
X-RAY DIFFRACTIONr_mcangle_it1.42523516
X-RAY DIFFRACTIONr_scbond_it2.3131454
X-RAY DIFFRACTIONr_scangle_it3.2524.51213
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 186 -
Rwork0.337 3570 -
all-3756 -
obs--95.26 %

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