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

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Basic information

Entry
Database: PDB / ID: 3oaz
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 / Chem-2M5
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 1.3Jul 29, 2020Group: Data collection / Derived calculations / Category: chem_comp / struct_site / struct_site_gen / Item: _chem_comp.mon_nstd_flag / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)96,16744
Polymers93,8374
Non-polymers2,33040
Water18,0691003
1
H: Fab 2G12, heavy chain
K: Fab 2G12, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,16121
Polymers46,9182
Non-polymers1,24319
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-14 kcal/mol
Surface area21540 Å2
MethodPISA
2
L: Fab 2G12, light chain
M: Fab 2G12, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,00623
Polymers46,9182
Non-polymers1,08721
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-13 kcal/mol
Surface area21790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.623, 72.092, 84.074
Angle α, β, γ (deg.)90.00, 95.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 4 molecules HMKL

#1: Antibody Fab 2G12, heavy chain


Mass: 23716.609 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, light chain


Mass: 23201.840 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)

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Sugars , 1 types, 2 molecules

#5: Sugar ChemComp-2M5 / methyl 7-deoxy-L-glycero-alpha-D-manno-heptopyranoside / methyl 7-deoxy-L-glycero-alpha-D-manno-heptoside / methyl 7-deoxy-L-glycero-D-manno-heptoside / methyl 7-deoxy-L-glycero-manno-heptoside


Type: D-saccharide / Mass: 208.209 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H16O6

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Non-polymers , 3 types, 1041 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1003 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 47.29 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.75→29.65 Å / Num. obs: 85554

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1OP3

1op3
PDB Unreleased entry


Resolution: 1.75→29.65 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 4.91 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 4297 5 %RANDOM
Rwork0.1761 ---
obs0.1782 85506 98.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 53.38 Å2 / Biso mean: 23.494 Å2 / Biso min: 2.47 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å20 Å2-0.91 Å2
2--0.82 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6534 0 116 1003 7653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227052
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.9649658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5175950
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66924.113265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.927151140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7191530
X-RAY DIFFRACTIONr_chiral_restr0.0960.21141
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215210
X-RAY DIFFRACTIONr_mcbond_it0.7451.54445
X-RAY DIFFRACTIONr_mcangle_it1.33827261
X-RAY DIFFRACTIONr_scbond_it2.39332607
X-RAY DIFFRACTIONr_scangle_it3.5414.52340
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 289 -
Rwork0.249 5736 -
all-6025 -
obs--94.05 %
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)
11.1260.5418-0.19151.4004-0.72881.3060.00570.0203-0.00430.08410.0187-0.0443-0.0576-0.0167-0.02440.0590.0245-0.00780.01190.00010.011663.2126-6.945938.7264
20.805-0.1360.29471.1995-0.45331.07710.0155-0.0057-0.10750.06630.00580.0610.05760.0068-0.02120.0426-0.00060.01490.0458-0.05660.09374.2728-19.472614.3814
31.9575-0.10631.52291.0351-0.18782.7506-0.2132-0.32770.18060.1070.02310.1617-0.3037-0.51780.19010.07750.0405-0.01180.1098-0.03330.066753.2221.688223.0195
42.21650.8725-0.06771.5052-0.09671.049-0.02030.10780.0308-0.2187-0.0973-0.1052-0.00620.15910.11760.07920.02980.01810.05080.01870.064816.8549.85010.5602
53.19890.27320.72831.270.1291.37620.0229-0.0886-0.13630.0573-0.05880.06360.06070.04260.03590.0179-0.00650.0140.03660.00630.021424.1157-18.091422.6388
62.4155-0.05320.49781.01140.14640.86560.04530.0722-0.08370.0368-0.02010.02080.0748-0.0359-0.02520.04520.02450.00630.06820.02170.012743.8178-12.450632.6663
71.7771-0.41510.61821.2774-0.48741.4869-0.036-0.09010.12110.035-0.0176-0.1024-0.143-0.00770.05360.06410.01-0.00350.0148-0.00590.046314.177916.182214.8468
83.07130.11860.251.7839-0.50111.95150.07290.091-0.1321-0.07420.03940.13660.0835-0.1891-0.11230.0548-0.0122-0.01140.03390.02220.047353.557812.87958.8108
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L1 - 107
2X-RAY DIFFRACTION2K1 - 107
3X-RAY DIFFRACTION3L111 - 211
4X-RAY DIFFRACTION4K111 - 213
5X-RAY DIFFRACTION5M1 - 112
6X-RAY DIFFRACTION6H1 - 112
7X-RAY DIFFRACTION7H117 - 227
8X-RAY DIFFRACTION8M117 - 226

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