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- PDB-5jop: Crystal structure of anti-glycan antibody Fab14.22 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5jop
TitleCrystal structure of anti-glycan antibody Fab14.22 in complex with Streptococcus pneumoniae serotype 14 tetrasaccharide at 1.75 A
Components
  • Fab 14.22 light chain
  • Fab14.22 heavy chain
KeywordsIMMUNE SYSTEM / S. pneumoniae serotype 14 / anti-glycan B cells / synthetic conjugate vaccine / nanomolar affinity anti-glycan antibody / immune system-bacterial glycan complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSarkar, A. / Irimia, A. / Teyton, L. / Wilson, I.A.
CitationJournal: J. Clin. Invest. / Year: 2017
Title: T cells control the generation of nanomolar-affinity anti-glycan antibodies.
Authors: Polonskaya, Z. / Deng, S. / Sarkar, A. / Kain, L. / Comellas-Aragones, M. / McKay, C.S. / Kaczanowska, K. / Holt, M. / McBride, R. / Palomo, V. / Self, K.M. / Taylor, S. / Irimia, A. / ...Authors: Polonskaya, Z. / Deng, S. / Sarkar, A. / Kain, L. / Comellas-Aragones, M. / McKay, C.S. / Kaczanowska, K. / Holt, M. / McBride, R. / Palomo, V. / Self, K.M. / Taylor, S. / Irimia, A. / Mehta, S.R. / Dan, J.M. / Brigger, M. / Crotty, S. / Schoenberger, S.P. / Paulson, J.C. / Wilson, I.A. / Savage, P.B. / Finn, M.G. / Teyton, L.
History
DepositionMay 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_validate_symm_contact / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_seq_id_1 / _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.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 27, 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
D: Fab 14.22 light chain
E: Fab14.22 heavy chain
L: Fab 14.22 light chain
H: Fab14.22 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,88728
Polymers102,4294
Non-polymers3,45924
Water18,5371029
1
D: Fab 14.22 light chain
E: Fab14.22 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,94114
Polymers51,2142
Non-polymers1,72612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
L: Fab 14.22 light chain
H: Fab14.22 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,94614
Polymers51,2142
Non-polymers1,73212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.267, 74.740, 120.304
Angle α, β, γ (deg.)90.00, 100.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Antibody , 2 types, 4 molecules DLEH

#1: Antibody Fab 14.22 light chain


Mass: 24436.193 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): B cell hybridoma / Production host: Mus musculus (house mouse)
#2: Antibody Fab14.22 heavy chain


Mass: 26778.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): B cell hybridoma / Production host: Mus musculus (house mouse)

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Sugars , 1 types, 2 molecules

#3: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose-(1-6)-[beta-D-galactopyranose-(1-4)]2-acetamido-2- ...beta-D-galactopyranose-(1-4)-beta-D-glucopyranose-(1-6)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 707.630 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpb1-6[DGalpb1-4]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a2122h-1b_1-5]/1-2-3-2/a4-b1_a6-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}[(6+1)][b-D-Glcp]{[(4+1)][b-D-Galp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 1051 molecules

#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1029 / 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: 2.7 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.8 M NaHPO4/1.2 M K2HPO4, 0.1M sodium acetate (pH 4.5), and 5% Jeffamine 900

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→47.19 Å / Num. obs: 106772 / % possible obs: 97 % / Redundancy: 2.7 % / Biso Wilson estimate: 22.3 Å2 / CC1/2: 0.93 / Rsym value: 0.065 / Net I/σ(I): 11.4
Reflection shellResolution: 1.75→1.7692 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 1.4 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: 000)refinement
HKL-2000v706edata reduction
HKL-2000v706edata scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QGC

1qgc


Resolution: 1.75→47.184 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1999 5337 5 %
Rwork0.1654 --
obs0.1671 106745 96.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→47.184 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6606 0 222 1032 7860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0147263
X-RAY DIFFRACTIONf_angle_d1.3679946
X-RAY DIFFRACTIONf_dihedral_angle_d12.7214276
X-RAY DIFFRACTIONf_chiral_restr0.1121126
X-RAY DIFFRACTIONf_plane_restr0.0091247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7493-1.76920.31911750.28113313X-RAY DIFFRACTION95
1.7692-1.790.31531800.26553424X-RAY DIFFRACTION98
1.79-1.81180.27881810.26123445X-RAY DIFFRACTION99
1.8118-1.83480.29051800.24623408X-RAY DIFFRACTION99
1.8348-1.85890.27791790.2443419X-RAY DIFFRACTION99
1.8589-1.88440.28421820.2353435X-RAY DIFFRACTION99
1.8844-1.91130.27571810.22723449X-RAY DIFFRACTION99
1.9113-1.93980.23761790.213401X-RAY DIFFRACTION99
1.9398-1.97020.23271840.19743501X-RAY DIFFRACTION99
1.9702-2.00250.23651770.18113367X-RAY DIFFRACTION99
2.0025-2.0370.20671830.18043459X-RAY DIFFRACTION99
2.037-2.0740.20611810.18523430X-RAY DIFFRACTION99
2.074-2.11390.23161790.17683413X-RAY DIFFRACTION99
2.1139-2.15710.19831800.17483425X-RAY DIFFRACTION98
2.1571-2.2040.20981820.17043446X-RAY DIFFRACTION98
2.204-2.25520.20311780.16763402X-RAY DIFFRACTION98
2.2552-2.31160.21021790.1653393X-RAY DIFFRACTION98
2.3116-2.37410.22581800.17013419X-RAY DIFFRACTION98
2.3741-2.4440.2111790.17353406X-RAY DIFFRACTION98
2.444-2.52290.23951800.1763410X-RAY DIFFRACTION97
2.5229-2.6130.25141760.17593379X-RAY DIFFRACTION97
2.613-2.71770.21541780.17123366X-RAY DIFFRACTION97
2.7177-2.84130.20371770.15973356X-RAY DIFFRACTION96
2.8413-2.99110.18931750.15733341X-RAY DIFFRACTION95
2.9911-3.17850.18481770.15583358X-RAY DIFFRACTION96
3.1785-3.42380.17841730.1483285X-RAY DIFFRACTION94
3.4238-3.76820.14711730.13733292X-RAY DIFFRACTION93
3.7682-4.31320.16321730.12473275X-RAY DIFFRACTION93
4.3132-5.43290.14681680.12623212X-RAY DIFFRACTION91
5.4329-47.2010.20231680.17853179X-RAY DIFFRACTION88
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)
10.73080.22150.05360.0274-0.00394.1677-0.0501-0.02570.1202-0.0075-0.0046-0.0218-0.11820.30670.04930.15890.0411-0.020.13120.00110.2403-10.537959.646719.7555
21.36541.4030.93045.03473.76494.12080.1053-0.12210.14330.0222-0.23860.1046-0.033-0.33730.16610.03240.0706-0.03120.18040.02840.0987-29.349749.921831.1768
30.50740.1357-0.32170.32560.41792.9870.0354-0.00050.0229-0.0690.1311-0.0108-0.017-0.0917-0.16570.16450.036-0.01830.12860.02350.1908-27.829756.115314.9552
41.4871-0.28710.86320.44580.15571.24130.0246-0.06130.077-0.0447-0.0222-0.04770.0488-0.03880.00140.14650.01360.03110.1296-0.01140.1241-12.03737.763839.8819
51.20320.11841.52370.25190.26242.33020.09980.0512-0.12990.06460.048-0.04770.2180.2106-0.15290.19820.0540.00590.1865-0.04820.1774-4.839725.587529.3939
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN E AND RESID 1:212 )E1 - 212
2X-RAY DIFFRACTION2( CHAIN D AND RESID 301:304 ) OR ( CHAIN L AND RESID 301:304 )D301 - 304
3X-RAY DIFFRACTION2( CHAIN D AND RESID 301:304 ) OR ( CHAIN L AND RESID 301:304 )L301 - 304
4X-RAY DIFFRACTION3( CHAIN D AND RESID 1:213 )D1 - 213
5X-RAY DIFFRACTION4( CHAIN L AND RESID 1:213 )L1 - 213
6X-RAY DIFFRACTION5( CHAIN H AND RESID 1:212 )H1 - 212

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