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- PDB-3sy0: S25-2- A(2-8)-A(2-4)KDO trisaccharide complex -

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Basic information

Entry
Database: PDB / ID: 3sy0
TitleS25-2- A(2-8)-A(2-4)KDO trisaccharide complex
Components(S25-2 FAB (IGG1K) ...) x 2
KeywordsIMMUNE SYSTEM / antigen-binding fragment / FAB / anti-carbohydrate / anti-LPS / antibody / immunoglobulin / KDO
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.489 Å
AuthorsNguyen, H.P. / Seto, N.O. / Mackenzie, C.R. / Brade, L. / Kosma, P. / Brade, H. / Evans, S.V.
CitationJournal: NAT.STRUCT.BIOL. / Year: 2003
Title: Germline antibody recognition of distinct carbohydrate epitopes
Authors: Nguyen, H.P. / Seto, N.O. / Mackenzie, C.R. / Brade, L. / Kosma, P. / Brade, H. / Evans, S.V.
History
DepositionJul 15, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionAug 3, 2011ID: 1Q9Q
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 2.0Jul 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_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 / struct_asym / struct_conn / 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.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 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 2.2Nov 20, 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: S25-2 FAB (IGG1K) light chain
B: S25-2 FAB (IGG1K) heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1866
Polymers48,3542
Non-polymers8334
Water12,755708
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-58 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.600, 80.900, 130.600
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 S25-2 FAB (IGG1K) light chain


Mass: 24242.898 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody S25-2 FAB (IGG1K) heavy chain


Mass: 24110.967 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

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Sugars , 1 types, 1 molecules

#3: Polysaccharide 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-8)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic ...3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-8)-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_b8-c2WURCSPDB2Glycan 1.1.0
[][propyl]{[(1+2)][a-D-Kdop]{[(4+2)][a-D-Kdop]{[(8+2)][a-D-Kdop]{}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 711 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


Mass: 18.015 Da / Num. of mol.: 708 / 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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: KDO trisaccharide, magnesium chloride, zinc chloride, ethylene glycol, glycerol, PEG 4000, TRIS, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.15 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 10, 2001 / Details: mirrors
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 1.49→19.77 Å / Num. obs: 73625

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: STARTING MODEL: PDB ENTRY 1Q9O, S45-18 FAB UNLIGANDED

1q9o


Resolution: 1.489→19.773 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8676 / SU ML: 0.35 / σ(F): 1 / Phase error: 20.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2121 7420 10.08 %
Rwork0.187 --
obs0.1895 73626 92.11 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.464 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 63.34 Å2 / Biso mean: 22.3333 Å2 / Biso min: 8.22 Å2
Baniso -1Baniso -2Baniso -3
1-3.9283 Å2-0 Å2-0 Å2
2---1.878 Å2-0 Å2
3----2.0503 Å2
Refinement stepCycle: LAST / Resolution: 1.489→19.773 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3399 0 52 708 4159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083543
X-RAY DIFFRACTIONf_angle_d1.24808
X-RAY DIFFRACTIONf_chiral_restr0.074543
X-RAY DIFFRACTIONf_plane_restr0.005607
X-RAY DIFFRACTIONf_dihedral_angle_d12.2841270
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4887-1.50560.28051690.26561534170366
1.5056-1.52330.30831780.25411817199574
1.5233-1.54190.27062210.23891866208781
1.5419-1.56140.2462210.22372076229787
1.5614-1.58190.25532350.21422120235590
1.5819-1.60360.22152480.2072135238390
1.6036-1.62650.24812470.19252160240791
1.6265-1.65080.20912440.19352154239891
1.6508-1.67650.2292260.20082184241092
1.6765-1.7040.22652560.19562205246193
1.704-1.73340.21772750.18552175245094
1.7334-1.76490.24252540.19222272252694
1.7649-1.79880.24132690.18782205247495
1.7988-1.83550.21752530.18422260251395
1.8355-1.87540.21532880.18562242253095
1.8754-1.9190.20922500.19112265251595
1.919-1.96690.21532450.18292323256897
1.9669-2.020.2252590.1832302256197
2.02-2.07940.18432440.18332339258396
2.0794-2.14650.20822500.1852332258298
2.1465-2.22310.20532600.1842307256797
2.2231-2.3120.23052560.19142350260697
2.312-2.4170.21672470.18472335258297
2.417-2.54420.22192590.19792326258596
2.5442-2.70320.21782360.18992372260897
2.7032-2.91130.22142980.19562284258296
2.9113-3.20320.20592580.1872344260296
3.2032-3.66420.19272460.17872343258995
3.6642-4.60680.18992900.15682303259394
4.6068-19.77440.20552380.19512276251487

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