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- PDB-3ob0: A non-self sugar mimic of the HIV glycan shield shows enhanced an... -

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Basic information

Entry
Database: PDB / ID: 3ob0
TitleA non-self sugar mimic of the HIV glycan shield shows enhanced antigenicity
Components
  • Fab 2G12, heavy chain
  • Fab 2G12, light chain
KeywordsIMMUNE SYSTEM / Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsDoores, K.J. / Fulton, Z. / Hong, V. / Patel, M.K. / Scanlan, C.N. / Wormald, M.R. / Finn, M.G. / Burton, D.R. / Wilson, I.A. / Davis, B.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: A nonself sugar mimic of the HIV glycan shield shows enhanced antigenicity.
Authors: Doores, K.J. / Fulton, Z. / Hong, V. / Patel, M.K. / Scanlan, C.N. / Wormald, M.R. / Finn, M.G. / Burton, D.R. / Wilson, I.A. / Davis, B.G.
History
DepositionAug 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / 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_validate_close_contact / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _entity.src_method / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 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
L: Fab 2G12, light chain
H: Fab 2G12, heavy chain
K: Fab 2G12, light chain
M: Fab 2G12, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4566
Polymers94,0954
Non-polymers1,3612
Water1448
1
L: Fab 2G12, light chain
M: Fab 2G12, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7283
Polymers47,0482
Non-polymers6811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-9 kcal/mol
Surface area21790 Å2
MethodPISA
2
H: Fab 2G12, heavy chain
K: Fab 2G12, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7283
Polymers47,0482
Non-polymers6811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-10 kcal/mol
Surface area21760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.740, 131.155, 169.534
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Fab 2G12, light chain


Mass: 23201.840 Da / Num. of mol.: 2 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ (production host): ovary / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Fab 2G12, heavy chain


Mass: 23845.791 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ (production host): ovary / Production host: Cricetulus griseus (Chinese hamster)
#3: Polysaccharide 7-deoxy-L-glycero-alpha-D-manno-heptopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D- ...7-deoxy-L-glycero-alpha-D-manno-heptopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 680.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,4,3/[a1122h-1a_1-5][a11221m-1a_1-5]/1-1-1-2/a3-b1_b2-c1_c2-d1WURCSPDB2Glycan 1.1.0
[][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-7-deoxy-Manp]{}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.64 Å3/Da / Density % sol: 53.46 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.85→30 Å / Num. obs: 21555 / Biso Wilson estimate: 59.67 Å2

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.1data extraction
BUSTER2.8.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1OP3

1op3
PDB Unreleased entry


Resolution: 2.85→30 Å / Cor.coef. Fo:Fc: 0.8658 / Cor.coef. Fo:Fc free: 0.8403 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2797 1045 4.89 %RANDOM
Rwork0.2322 ---
obs0.2345 21374 --
Displacement parametersBiso max: 229.74 Å2 / Biso mean: 79.1252 Å2 / Biso min: 36.04 Å2
Baniso -1Baniso -2Baniso -3
1--29.4222 Å20 Å20 Å2
2---9.5095 Å20 Å2
3---38.9317 Å2
Refine analyzeLuzzati coordinate error obs: 0.496 Å
Refinement stepCycle: LAST / Resolution: 2.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6535 0 92 8 6635
LS refinement shellResolution: 2.85→2.99 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.319 100 4.97 %
Rwork0.2921 1911 -
all0.2935 2011 -

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