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- PDB-3t65: S25-2- A(2-8)KDO disaccharide complex -

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Basic information

Entry
Database: PDB / ID: 3t65
TitleS25-2- A(2-8)KDO disaccharide 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: 1.45 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 28, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionAug 17, 2011ID: 1Q9R
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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 / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_atom_id ..._atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
B: S25-2 FAB (IGG1K) heavy chain
A: S25-2 FAB (IGG1K) light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9425
Polymers48,3542
Non-polymers5883
Water13,259736
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-51 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.900, 81.600, 131.500
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 BA

#1: 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)
#2: 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)

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Sugars , 1 types, 1 molecules

#3: Polysaccharide 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-8)-prop-2-en-1-yl 3-deoxy-alpha-D-manno-oct-2- ...3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-8)-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/a8-b2WURCSPDB2Glycan 1.1.0
[][propyl]{[(1+2)][a-D-Kdop]{[(8+2)][a-D-Kdop]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 738 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / 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.: 736 / 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: 51.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: KDO disaccharide, 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: Jan 1, 2003 / 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: 1.45→19.78 Å / Num. obs: 82096

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→19.775 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.88 / SU ML: 0.36 / σ(F): 1 / Phase error: 19.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2113 8262 10.06 %
Rwork0.1926 --
obs0.1945 82096 92.89 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.419 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso max: 63.85 Å2 / Biso mean: 20.1545 Å2 / Biso min: 7.49 Å2
Baniso -1Baniso -2Baniso -3
1-2.4695 Å2-0 Å2-0 Å2
2---0.6905 Å2-0 Å2
3----1.779 Å2
Refinement stepCycle: LAST / Resolution: 1.45→19.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3399 0 36 736 4171
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073524
X-RAY DIFFRACTIONf_angle_d1.1464785
X-RAY DIFFRACTIONf_chiral_restr0.07539
X-RAY DIFFRACTIONf_plane_restr0.005606
X-RAY DIFFRACTIONf_dihedral_angle_d12.2911262
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 (%)
1.4498-1.46630.24542910.21642444273593
1.4663-1.48350.26872380.26382183242183
1.4835-1.50160.24812740.21212425269994
1.5016-1.52060.24952830.222399268292
1.5206-1.54060.24422680.21792425269392
1.5406-1.56170.22662970.19432485278296
1.5617-1.5840.21452640.18512573283796
1.584-1.60760.21523260.18692471279797
1.6076-1.63270.23412440.18592620286497
1.6327-1.65950.21713060.18622501280797
1.6595-1.68810.20082590.18292560281997
1.6881-1.71880.22862830.18732575285898
1.7188-1.75180.19342870.17922562284998
1.7518-1.78750.22692750.18622584285998
1.7875-1.82640.19822900.17982591288198
1.8264-1.86880.19832530.17742593284697
1.8688-1.91550.23832440.22222092233679
1.9155-1.96730.222660.23092258252487
1.9673-2.02510.19712960.18932616291299
2.0251-2.09040.21222670.18152637290498
2.0904-2.1650.20312810.18332617289899
2.165-2.25160.21451820.19641838202069
2.2516-2.35390.22382360.19322013224976
2.3539-2.47780.21652860.19242648293499
2.4778-2.63270.23052980.198426702968100
2.6327-2.83540.20693170.198226582975100
2.8354-3.11980.22133330.198426402973100
3.1198-3.56890.20373240.18932674299899
3.5689-4.48780.18792000.16931709190963
4.4878-19.7770.19442940.19322773306796

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