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- PDB-2r1x: Crystal structure of S25-2 Fab in complex with Kdo analogues -

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Basic information

Entry
Database: PDB / ID: 2r1x
TitleCrystal structure of S25-2 Fab in complex with Kdo analogues
Components(Fab, antibody fragment (IgG1k), ...) x 2
KeywordsIMMUNE SYSTEM / Fab / anti-carbohydrate antibody
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / blood microparticle / 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 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: 1.6 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 2.0Apr 22, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / struct_conn
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 / _chem_comp.type / _struct_conn.pdbx_leaving_atom_flag
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 / database_PDB_caveat / 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 / pdbx_validate_chiral / 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 / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_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.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)48,9326
Polymers48,3542
Non-polymers5784
Water6,738374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-56 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.940, 81.490, 131.420
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) / References: UniProt: Q52L64*PLUS
#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) / References: UniProt: A2NU21*PLUS

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Sugars , 1 types, 1 molecules

#3: Polysaccharide 2,6-anhydro-3,5-dideoxy-D-ribo-oct-2-enonic acid-(4-8)-prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2- ...2,6-anhydro-3,5-dideoxy-D-ribo-oct-2-enonic acid-(4-8)-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][AEe2d22h_2-6]/1-2/a8-b4WURCSPDB2Glycan 1.1.0
[][propyl]{[(1+2)][a-D-Kdop]{}}LINUCSPDB-CARE

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Non-polymers , 3 types, 377 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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.: 374 / 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: 2.54 Å3/Da / Density % sol: 51.64 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 8
Details: PEG 4000, ethelyene glycol, pH 8.0, vapour diffusion, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.5→19.91 Å / Num. obs: 76352 / % possible obs: 95.7 % / Redundancy: 3.28 % / Rmerge(I) obs: 0.035 / Χ2: 0.96 / Net I/σ(I): 15.9 / Scaling rejects: 1894
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.5-1.552.210.2852.71473566541.0884.6
1.55-1.623.040.2593.42382478111.1199.1
1.62-1.693.20.21842532178721.199.6
1.69-1.783.250.17952582178711.0899.3
1.78-1.893.310.1366.52599277851.0198.7
1.89-2.043.350.18.82633377790.9297.9
2.04-2.243.230.06712.22495876830.8696.7
2.24-2.563.240.04816.52509377040.8495.9
2.56-3.233.630.0327.62791276480.8194.8
3.23-19.914.250.0254.93246375450.9190.3

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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
CrystalCleardata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→19.9 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.65 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.239 3246 5.1 %RANDOM
Rwork0.217 ---
obs0.218 63758 96.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.655 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2---0.05 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3349 0 35 374 3758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223466
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.9624720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3095431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.88623.796137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.04815554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5921517
X-RAY DIFFRACTIONr_chiral_restr0.110.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022599
X-RAY DIFFRACTIONr_nbd_refined0.2080.21556
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22383
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2306
X-RAY DIFFRACTIONr_metal_ion_refined0.0440.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.223
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0220.21
X-RAY DIFFRACTIONr_mcbond_it0.9411.52206
X-RAY DIFFRACTIONr_mcangle_it1.48123508
X-RAY DIFFRACTIONr_scbond_it2.36131455
X-RAY DIFFRACTIONr_scangle_it3.2554.51212
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.452 235 -
Rwork0.393 4551 -
all-4786 -
obs--99.73 %

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