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- PDB-4m7j: Crystal structure of S25-26 in complex with Kdo(2.8)Kdo(2.4)Kdo t... -

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Basic information

Entry
Database: PDB / ID: 4m7j
TitleCrystal structure of S25-26 in complex with Kdo(2.8)Kdo(2.4)Kdo trisaccharide
Components
  • S25-26 Fab (IgG1k) heavy chain
  • S25-26 Fab (Igg1k) light chain
KeywordsIMMUNE SYSTEM / Beta-Sandwich / Carbohydrate/Sugar Binding
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsHaji-Ghassemi, O. / Evans, S.V. / Muller-Loennies, S. / Saldova, R. / Muniyappa, M. / Brade, L. / Rudd, P.M. / Harvey, D.J. / Kosma, P. / Brade, H.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Groove-type Recognition of Chlamydiaceae-specific Lipopolysaccharide Antigen by a Family of Antibodies Possessing an Unusual Variable Heavy Chain N-Linked Glycan.
Authors: Haji-Ghassemi, O. / Muller-Loennies, S. / Saldova, R. / Muniyappa, M. / Brade, L. / Rudd, P.M. / Harvey, D.J. / Kosma, P. / Brade, H. / Evans, S.V.
History
DepositionAug 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Jul 9, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
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 / pdbx_struct_special_symmetry / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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 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
H: S25-26 Fab (IgG1k) heavy chain
L: S25-26 Fab (Igg1k) light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9736
Polymers47,8882
Non-polymers1,0854
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-21 kcal/mol
Surface area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.464, 74.464, 149.893
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11L-301-

PEG

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody S25-26 Fab (IgG1k) heavy chain


Mass: 23531.480 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: Balb/C
#2: Antibody S25-26 Fab (Igg1k) light chain


Mass: 24356.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Strain: Balb/C

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Sugars , 2 types, 2 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
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 221 molecules

#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M potassium chloride, 0.05M HEPES, 35% (v/v) pentaerythritol propoxylate (5/4 PO/OH), pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9794 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 23, 2011 / Details: Vertical focusing mirror
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. obs: 35967 / % possible obs: 99.9 % / Observed criterion σ(I): 2.2 / Redundancy: 13.7 % / Rmerge(I) obs: 0.064 / Χ2: 1.064 / Net I/σ(I): 11
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-2.0212.80.55635580.9271100
2.02-2.114.10.41535070.9721100
2.1-2.214.20.31935651.0361100
2.2-2.3114.10.22235281.0571100
2.31-2.4614.20.17635681.0641100
2.46-2.65140.13235731.2021100
2.65-2.9113.90.09635831.1991100
2.91-3.3313.90.06236051.0891100
3.33-4.213.10.05736720.998199.9
4.2-2512.90.04638081.078199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MacromolecularCrystallography Data Collector (MxDC)data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T2Q

1t2q


Resolution: 1.95→24.45 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.2723 / WRfactor Rwork: 0.2308 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7763 / SU B: 10.632 / SU ML: 0.166 / SU R Cruickshank DPI: 0.1818 / SU Rfree: 0.1603 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1793 5 %RANDOM
Rwork0.2117 ---
obs0.2134 35920 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.71 Å2 / Biso mean: 63.074 Å2 / Biso min: 34.87 Å2
Baniso -1Baniso -2Baniso -3
1-1.57 Å21.57 Å2-0 Å2
2--1.57 Å2-0 Å2
3----5.08 Å2
Refinement stepCycle: LAST / Resolution: 1.95→24.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3368 0 71 219 3658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.023530
X-RAY DIFFRACTIONr_bond_other_d0.0030.023216
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.9654818
X-RAY DIFFRACTIONr_angle_other_deg0.8423.0067436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3135436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.80424.088137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.12315548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2611514
X-RAY DIFFRACTIONr_chiral_restr0.0820.2549
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213934
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02790
X-RAY DIFFRACTIONr_mcbond_it1.6352.9741750
X-RAY DIFFRACTIONr_mcbond_other1.6332.9711749
X-RAY DIFFRACTIONr_mcangle_it2.4834.452184
LS refinement shellResolution: 1.95→1.999 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 130 -
Rwork0.288 2455 -
all-2585 -
obs--99.42 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.5122-0.2059-2.25091.4356-0.25985.8961-0.12880.12070.05750.1420.0512-0.00930.15210.040.07770.1861-0.076-0.02670.0717-0.01360.0736-1.286838.9629-1.4275
21.9431.30070.74455.4884-0.5114.6093-0.0903-0.2924-0.9606-0.32830.1128-0.57630.79550.1004-0.02250.38940.13840.09840.14740.13930.5393-6.322522.463730.2456
32.67573.63360.64089.4637-2.00874.6166-0.1768-0.3619-1.0385-0.16010.1742-1.06120.58290.19320.00260.48030.22760.2430.36750.25480.6037-4.305320.340230.5702
41.61041.3048-1.11255.0138-1.32491.5067-0.41280.3604-0.50410.08170.17390.36520.627-0.12010.23880.5839-0.31540.22610.445-0.18010.3148-9.014520.8976-8.5307
510.3114-2.811-8.72521.1011.204511.5281-0.89750.0810.26440.380.0442-0.39590.1421-0.32040.85330.9504-0.15910.17020.2434-0.19730.5775-12.3115.24038.2002
62.38631.0561-0.80023.53611.03653.3457-0.30610.0973-0.3784-0.60340.0658-0.25380.4343-0.30940.24040.5094-0.01070.07220.0814-0.00710.1787-20.299317.970227.052
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H1 - 116
2X-RAY DIFFRACTION2H117 - 164
3X-RAY DIFFRACTION3H165 - 214
4X-RAY DIFFRACTION4L1 - 109
5X-RAY DIFFRACTION5L110 - 115
6X-RAY DIFFRACTION6L116 - 214

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