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- PDB-4hij: Anti-Streptococcus pneumoniae 23F Fab 023.102 with bound L-rhamno... -

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Basic information

Entry
Database: PDB / ID: 4hij
TitleAnti-Streptococcus pneumoniae 23F Fab 023.102 with bound L-rhamnose-(1-2)-alpha-D-galactose-(3-O)-phosphate-2-glycerol
Components
  • Fab 023.102 heavy chain
  • Fab 023.102 light chain
KeywordsIMMUNE SYSTEM / Immunoglobin / Antibody / Streptococcus pneumoniae 23F
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBryson, S. / Risnes, L. / Damgupta, S. / Thomson, C.A. / Schrader, J.W. / Pai, E.F.
CitationJournal: J. Immunol. / Year: 2016
Title: Structures of Preferred Human IgV Genes-Based Protective Antibodies Identify How Conserved Residues Contact Diverse Antigens and Assign Source of Specificity to CDR3 Loop Variation.
Authors: Bryson, S. / Thomson, C.A. / Risnes, L.F. / Dasgupta, S. / Smith, K. / Schrader, J.W. / Pai, E.F.
History
DepositionOct 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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_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_special_symmetry.label_asym_id / _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.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

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Assembly

Deposited unit
A: Fab 023.102 light chain
B: Fab 023.102 heavy chain
C: Fab 023.102 light chain
D: Fab 023.102 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,89010
Polymers97,8354
Non-polymers1,0556
Water5,747319
1
A: Fab 023.102 light chain
B: Fab 023.102 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4455
Polymers48,9172
Non-polymers5273
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-22 kcal/mol
Surface area18590 Å2
MethodPISA
2
C: Fab 023.102 light chain
D: Fab 023.102 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4455
Polymers48,9172
Non-polymers5273
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-19 kcal/mol
Surface area18510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.870, 66.488, 118.214
Angle α, β, γ (deg.)90.00, 111.58, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-357-

HOH

DetailsFab Fragment

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Components

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody Fab 023.102 light chain


Mass: 23801.338 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pARC / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue
#2: Antibody Fab 023.102 heavy chain


Mass: 25116.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pARC / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue

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Sugars , 1 types, 2 molecules

#3: Polysaccharide alpha-L-rhamnopyranose-(1-2)-methyl beta-D-galactopyranoside


Type: oligosaccharide / Mass: 340.323 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LRhapa1-2DGalp[1Me]b1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5_1*OC][a2211m-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-Galp]{[(2+1)][a-L-Rhap]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 323 molecules

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


Mass: 94.971 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.69 Å3/Da / Density % sol: 54.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.05M Na Citrate, pH 3-4, 18% PEG 3350, 0.2M Li Acetate , VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 14, 2010 / Details: Rigaku Osmic VariMax
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→17 Å / Num. all: 60892 / Num. obs: 55118 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.68 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 16.4
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 1.17 % / Rmerge(I) obs: 0.258 / Mean I/σ(I) obs: 2.8 / Num. unique all: 5329 / % possible all: 67.4

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Processing

Software
NameClassification
MAR345dtbdata collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HIE

4hie


Resolution: 2.1→17 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.262 2672 RANDOM
Rwork0.249 --
all0.249 60777 -
obs0.249 53389 -
Refinement stepCycle: LAST / Resolution: 2.1→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6311 0 64 319 6694
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007664
X-RAY DIFFRACTIONc_angle_deg1.71957

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