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- PDB-3t4y: S25-2- KDO monosaccharide complex -

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Basic information

Entry
Database: PDB / ID: 3t4y
TitleS25-2- KDO monosaccharide 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 / 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 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 26, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionAug 3, 2011ID: 1Q9V
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.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 1.2Sep 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 1.3Nov 27, 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)48,6825
Polymers48,3542
Non-polymers3283
Water10,269570
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-55 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.800, 81.400, 132.400
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

#4: Sugar ChemComp-KDO / 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid / 3-deoxy-d-manno-oct-2-ulopyranosonic acid / 2-keto-3-deoxy-D-mannooctanoic acid / 3-deoxy-alpha-D-manno-oct-2-ulosonic acid / 3-deoxy-D-manno-oct-2-ulosonic acid / 3-deoxy-manno-oct-2-ulosonic acid


Type: D-saccharide, alpha linking / Mass: 238.192 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H14O8
IdentifierTypeProgram
DKdopaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-KdopIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
KdoSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 572 molecules

#3: 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.: 570 / 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: 51.8 %
Crystal growTemperature: 293 K / Method: hanging drop / pH: 8
Details: KDO MONOSACCHARIDE, MAGNESIUM CHLORIDE, ZINC CHLORIDE, ETHYLENE GLYCOL, GLYCEROL, PEG 4000, TRIS, pH 8.0, 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: 1.73→19.97 Å / Num. obs: 43168

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q9R

1q9r
PDB Unreleased entry


Resolution: 1.73→19.452 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8652 / SU ML: 0.47 / σ(F): 1 / Phase error: 20.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2251 4342 10.06 %
Rwork0.1951 --
obs0.1981 43168 81.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.371 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso max: 63.77 Å2 / Biso mean: 20.9531 Å2 / Biso min: 6.99 Å2
Baniso -1Baniso -2Baniso -3
1-5.8118 Å2-0 Å2-0 Å2
2---2.2594 Å2-0 Å2
3----3.5524 Å2
Refinement stepCycle: LAST / Resolution: 1.73→19.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3399 0 18 570 3987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073507
X-RAY DIFFRACTIONf_angle_d1.0654763
X-RAY DIFFRACTIONf_chiral_restr0.071535
X-RAY DIFFRACTIONf_plane_restr0.004605
X-RAY DIFFRACTIONf_dihedral_angle_d12.8321252
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 (%)
1.73-1.74760.28091520.25661240139280
1.7476-1.76810.28451220.25161326144884
1.7681-1.78970.29591500.25181333148385
1.7897-1.81230.29371480.2381308145686
1.8123-1.83610.26261680.22911378154687
1.8361-1.86130.30081590.23261354151388
1.8613-1.88780.27881400.22751358149887
1.8878-1.9160.3499820.331264973142
1.916-1.94590.26021180.27791074119269
1.9459-1.97780.22821480.20081370151888
1.9778-2.01180.22361490.18761384153390
2.0118-2.04840.23791840.18471417160192
2.0484-2.08770.22981540.18881433158791
2.0877-2.13030.25381470.18541435158292
2.1303-2.17660.2391650.19671436160191
2.1766-2.22710.25681240.20591134125880
2.2271-2.28270.349240.329323926318
2.2827-2.34440.24131630.19711367153089
2.3444-2.41320.22561490.1941471162091
2.4132-2.4910.19861730.18311413158693
2.491-2.57980.23111660.19861451161792
2.5798-2.68280.23031340.19011471160591
2.6828-2.80460.24211440.1881465160992
2.8046-2.9520.20851790.18791418159791
2.952-3.13620.22131630.19331425158889
3.1362-3.37720.22011470.18381415156288
3.3772-3.71490.20611410.18121106124769
3.7149-4.24760.17171370.16621177131473
4.2476-5.33320.16441630.15631354151783
5.3332-19.45290.24031490.20031425157482

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