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- PDB-4hgw: Crystal structure of S25-2 in complex with a 5,6-dehydro-Kdo disa... -

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Basic information

Entry
Database: PDB / ID: 4hgw
TitleCrystal structure of S25-2 in complex with a 5,6-dehydro-Kdo disaccharide
Components
  • Antibody Fab fragment, heavy chain
  • Antibody Fab fragment, light chain
KeywordsIMMUNE SYSTEM / antibody / LPS
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBrooks, C.L. / Evans, S.V.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Exploring the cross-reactivity of S25-2: complex with a 5,6-dehydro-Kdo disaccharide.
Authors: Brooks, C.L. / Wimmer, K. / Kosma, P. / Muller-Loennies, S. / Brade, L. / Brade, H. / Evans, S.V.
History
DepositionOct 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Apr 22, 2020Group: Data collection / Derived calculations / Category: chem_comp / struct_conn / Item: _chem_comp.type / _struct_conn.pdbx_leaving_atom_flag
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_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.name / _pdbx_struct_assembly_gen.asym_id_list / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 20, 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: Antibody Fab fragment, light chain
B: Antibody Fab fragment, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9655
Polymers48,3542
Non-polymers6113
Water10,539585
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-83 kcal/mol
Surface area19300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.710, 81.300, 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

#1: Antibody Antibody Fab fragment, 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) / Cell line (production host): hydridoma / Production host: mus musculus (house mouse)
#2: Antibody Antibody Fab fragment, 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) / Cell line (production host): hybridoma / Production host: mus musculus (house mouse)
#3: Polysaccharide 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-prop-2-en-1-yl 3,5-dideoxy-alpha-D-threo-oct- ...3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-prop-2-en-1-yl 3,5-dideoxy-alpha-D-threo-oct-5-en-2-ulopyranosidonic acid


Type: oligosaccharide / Mass: 480.418 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[Aad1eE2h-2a_2-6_2*OCC=C][Aad1122h-2a_2-6]/1-2/a4-b2WURCSPDB2Glycan 1.1.0
[][propyl]{[(1+2)][a-D-5-deoxy-Kdop]{[(4+2)][a-D-Kdop]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 585 / 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: 51.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8
Details: PEG 8000, MgCl, Tris, ZnCl, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 25, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→19.92 Å / Num. obs: 57408 / % possible obs: 95.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Χ2: 0.94 / Net I/σ(I): 12.4 / Scaling rejects: 1735
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.65-1.713.710.25342140857481.0597.6
1.71-1.783.890.2114.62251857581.0197.3
1.78-1.864.090.1665.72368757530.9897.6
1.86-1.964.340.1337.12514857480.9397.2
1.96-2.084.340.1078.82526157890.996.9
2.08-2.244.240.08910.62421756840.8896.1
2.24-2.464.010.07412.82297356940.8895.1
2.46-2.823.860.05816.52200056500.9194.1
2.82-3.553.730.043222160757240.994.4
3.55-19.923.760.033342246758601.0192.9

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata reduction
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3t77

3t77


Resolution: 1.65→19.92 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.8568 / SU ML: 0.16 / σ(F): 1.38 / Phase error: 20.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1978 2915 5.08 %
Rwork0.1761 --
obs0.1772 57382 95.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.35 Å2 / Biso mean: 29.158 Å2 / Biso min: 13.75 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3314 0 35 585 3934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153458
X-RAY DIFFRACTIONf_angle_d1.484699
X-RAY DIFFRACTIONf_chiral_restr0.073530
X-RAY DIFFRACTIONf_plane_restr0.005590
X-RAY DIFFRACTIONf_dihedral_angle_d12.2231230
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.649-1.6760.26341570.22062551270895
1.676-1.70490.24531370.20822580271797
1.7049-1.73590.27161580.20292594275297
1.7359-1.76930.26141300.2072610274097
1.7693-1.80530.27531210.20852601272297
1.8053-1.84460.27971250.21032628275398
1.8446-1.88750.26661430.19542597274097
1.8875-1.93460.22961410.19092601274297
1.9346-1.98690.22341570.192631278897
1.9869-2.04530.21921300.18312579270997
2.0453-2.11120.241320.17832589272196
2.1112-2.18660.17691210.18242605272696
2.1866-2.2740.18041380.17092610274896
2.274-2.37740.18641480.17342543269195
2.3774-2.50250.18191150.18212572268795
2.5025-2.65890.20831460.182549269594
2.6589-2.86370.22881480.17562562271094
2.8637-3.15090.20281310.17842577270895
3.1509-3.60450.17941420.17192597273994
3.6045-4.53240.1811480.15352619276794
4.5324-19.92350.15781470.16962672281992

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