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

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Basic information

Entry
Database: PDB / ID: 3oay
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 / beta-D-fructopyranose / MALONATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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 5, 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 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
K: Fab 2G12, light chain
M: Fab 2G12, heavy chain
H: Fab 2G12, heavy chain
L: Fab 2G12, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6608
Polymers94,0954
Non-polymers5644
Water10,178565
1
K: Fab 2G12, light chain
H: Fab 2G12, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3304
Polymers47,0482
Non-polymers2822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-11 kcal/mol
Surface area21710 Å2
MethodPISA
2
M: Fab 2G12, heavy chain
L: Fab 2G12, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3304
Polymers47,0482
Non-polymers2822
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-11 kcal/mol
Surface area22070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.905, 93.258, 169.602
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 Fab 2G12, light chain


Mass: 23201.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
#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)
#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Sugar ChemComp-BDF / beta-D-fructopyranose / Fructose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DFrupbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-fructopyranoseCOMMON NAMEGMML 1.0
b-D-FrupIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FruSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 3.27 Å3/Da / Density % sol: 62.43 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.95→30 Å / Num. obs: 81352

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0069refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 6.628 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 4103 5.1 %RANDOM
Rwork0.1818 ---
obs0.1838 81125 89.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.3 Å2 / Biso mean: 47.66 Å2 / Biso min: 28.01 Å2
Baniso -1Baniso -2Baniso -3
1-2.28 Å20 Å20 Å2
2--0.9 Å20 Å2
3----3.19 Å2
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6526 0 38 565 7129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0226869
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.9579374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6285899
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28723.977264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.594151107
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3191531
X-RAY DIFFRACTIONr_chiral_restr0.120.21085
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215121
X-RAY DIFFRACTIONr_mcbond_it0.711.54349
X-RAY DIFFRACTIONr_mcangle_it1.29327063
X-RAY DIFFRACTIONr_scbond_it2.27932520
X-RAY DIFFRACTIONr_scangle_it3.4334.52282
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 224 -
Rwork0.235 4107 -
all-4331 -
obs--65.78 %
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)
12.0864-1.57591.06662.825-1.44143.235-0.01660.06480.0734-0.1632-0.0195-0.1647-0.03720.17820.0361-0.1196-0.00420.0102-0.13460.02-0.197742.4462-2.4528-43.4569
22.0412-1.2888-1.49972.70310.88672.8295-0.0137-0.1208-0.04890.0612-0.0146-0.06870.18110.02350.0283-0.1568-0.02670.0092-0.1240.0067-0.20424.1215-24.438314.7231
32.4365-0.4521-2.09773.59-1.24445.5837-0.022-0.31560.08320.78460.45070.6112-0.6475-0.3386-0.42880.09220.09340.11620.03620.1294-0.069216.918418.913-31.5693
43.2885-1.05980.36152.737-1.55884.69830.38510.47140.3029-0.3095-0.17410.1845-0.3942-0.1064-0.2110.05640.06520.0703-0.11030.0112-0.12051.16880.79754.4901
52.2751-0.2851-0.66332.409-0.38753.30230.00820.0570.06730.01190.01580.0029-0.02350.005-0.024-0.15780.02440.0315-0.14840.0228-0.21330.6966-19.3766-4.9803
61.7884-0.6844-0.9362.49130.0483.1104-0.03170.0275-0.03870.0524-0.01090.10840.0806-0.01890.0426-0.16080.03120.0034-0.1470.0177-0.216538.3172-10.3423-23.9895
73.86380.4005-2.07943.33140.01267.42670.6806-0.14370.8846-0.0312-0.2054-0.1053-0.93280.2394-0.47520.2566-0.05730.2234-0.0966-0.01810.137713.782611.07867.1083
84.7517-0.8461.26454.8534-2.88127.4151-0.1530.1431-0.0123-0.28120.91361.1980.0277-1.4256-0.7606-0.0371-0.0771-0.03040.40440.38710.28676.58246.4208-34.0793
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 107
2X-RAY DIFFRACTION2K1 - 107
3X-RAY DIFFRACTION3L111 - 213
4X-RAY DIFFRACTION4K111 - 213
5X-RAY DIFFRACTION5M1 - 112
6X-RAY DIFFRACTION6H1 - 112
7X-RAY DIFFRACTION7H117 - 227
8X-RAY DIFFRACTION8M117 - 228

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