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- PDB-6vl8: Anti-PEG antibody 6-3 Fab fragment in complex with PEG -

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Basic information

Entry
Database: PDB / ID: 6vl8
TitleAnti-PEG antibody 6-3 Fab fragment in complex with PEG
Components
  • 6-3 Fab heavy chain
  • 6-3 Fab light chain
KeywordsIMMUNE SYSTEM / antibody / fab / PEG / anti-PEG / polymer / anti-drug
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsNicely, N.I. / Huckaby, J.T. / Lai, S.K. / Jacobs, T.M.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)F32DE026683 United States
National Science Foundation (NSF, United States)DMR-1810168 United States
National Science Foundation (NSF, United States)DGE-1650116 United States
David and Lucile Packard Foundation2013-39274 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL141934 United States
CitationJournal: Commun Chem / Year: 2020
Title: Structure of an anti-PEG antibody reveals an open ring that captures highly flexible PEG polymers
Authors: Huckaby, J.T. / Jacobs, T.M. / Li, Z. / Perna, R.J. / Wang, A. / Nicely, N.I. / Lai, S.K.
History
DepositionJan 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
A: 6-3 Fab heavy chain
B: 6-3 Fab light chain
C: 6-3 Fab heavy chain
D: 6-3 Fab light chain
E: 6-3 Fab heavy chain
F: 6-3 Fab light chain
H: 6-3 Fab heavy chain
L: 6-3 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,84413
Polymers195,2158
Non-polymers2,6295
Water9,566531
1
A: 6-3 Fab heavy chain
B: 6-3 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8663
Polymers48,8042
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-18 kcal/mol
Surface area19660 Å2
MethodPISA
2
C: 6-3 Fab heavy chain
D: 6-3 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0874
Polymers48,8042
Non-polymers1,2842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-20 kcal/mol
Surface area19850 Å2
MethodPISA
3
E: 6-3 Fab heavy chain
F: 6-3 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0253
Polymers48,8042
Non-polymers1,2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-33 kcal/mol
Surface area20150 Å2
MethodPISA
4
H: 6-3 Fab heavy chain
L: 6-3 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8663
Polymers48,8042
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-29 kcal/mol
Surface area19970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.108, 87.791, 116.074
Angle α, β, γ (deg.)90.000, 113.655, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Antibody
6-3 Fab heavy chain


Mass: 24736.875 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / Strain (production host): HEK293
#2: Antibody
6-3 Fab light chain


Mass: 24066.783 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / Strain (production host): HEK293
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEU / 2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL / PEG 8000 / Polyethylene glycol


Mass: 1221.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H112O28 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 531 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 54.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG 1500, 100 mM MMT buffer pH 6.5

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.42→41.93 Å / Num. obs: 78203 / % possible obs: 99.8 % / Redundancy: 6.1 % / Biso Wilson estimate: 36.45 Å2 / CC1/2: 0.98 / CC star: 0.995 / Net I/σ(I): 17.1
Reflection shellResolution: 2.42→2.48 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3823 / CC1/2: 0.92 / CC star: 0.98

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3o2v

3o2v


Resolution: 2.42→41.92 Å / SU ML: 0.2965 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.2328
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2403 2000 2.57 %
Rwork0.1845 75943 -
obs0.1859 77943 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.46 Å2
Refinement stepCycle: LAST / Resolution: 2.42→41.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13094 0 158 531 13783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008713573
X-RAY DIFFRACTIONf_angle_d0.941518405
X-RAY DIFFRACTIONf_chiral_restr0.05282040
X-RAY DIFFRACTIONf_plane_restr0.0062312
X-RAY DIFFRACTIONf_dihedral_angle_d17.28851909
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.42-2.480.31311350.26035152X-RAY DIFFRACTION95.43
2.48-2.550.30641460.24365418X-RAY DIFFRACTION99.64
2.55-2.630.31281400.22675427X-RAY DIFFRACTION99.86
2.63-2.710.30711450.21885405X-RAY DIFFRACTION99.77
2.71-2.810.29511390.21375462X-RAY DIFFRACTION99.79
2.81-2.920.31911530.21925440X-RAY DIFFRACTION99.88
2.92-3.050.28931360.21455425X-RAY DIFFRACTION99.77
3.05-3.210.28541380.21285423X-RAY DIFFRACTION99.45
3.21-3.420.25461500.19855459X-RAY DIFFRACTION99.89
3.42-3.680.23661410.18335432X-RAY DIFFRACTION99.75
3.68-4.050.21541410.17265487X-RAY DIFFRACTION99.8
4.05-4.630.17341440.14335462X-RAY DIFFRACTION99.4
4.63-5.830.18981470.14285489X-RAY DIFFRACTION99.54
5.84-41.920.20791450.16355462X-RAY DIFFRACTION97.33
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)
10.27074866536-0.32580455350.1240683858120.500683402319-0.8251268600042.870418446870.0503911885047-0.1968327628440.1297441916610.05635260190750.0422977456371-0.121335955143-0.1558064808680.727739249328-0.07126402947210.323024590047-0.0618787015988-0.02908772416930.540450997854-0.1075654886480.33860424940648.608285552626.837002184513.1284066977
27.481884831771.369919858424.396010206553.68584547041.628052484374.77374131661-0.1427768686-0.00638324419470.0959507805071-0.100744519792-0.05558665801190.00149540905646-0.30147053179-0.08208591659410.2097746357170.318275697081-0.03671154891760.02353169817440.3015906134180.02201259177470.24769416237235.866641937231.2235283397-15.8135951702
31.86017189386-0.196596624971.998430137221.49527258907-0.4365068310595.949594312410.0360534893640.131431748255-0.0809043583104-0.04896803459360.00336346836524-0.1063579884090.4053977230710.573897299922-0.0561966311850.3214711594530.0802574371775-0.05721283457650.356001792388-0.0576898025230.30039138297539.34967575165.7162774692711.0609622128
44.426000189672.48216615051-2.273916148434.05606514338-3.056153035734.28390740115-0.07393663122610.4572200532760.026546490469-0.3885046147370.0662034681087-0.2019279250220.2098271417360.112902014107-0.00284749286950.332723900810.01856184883610.01443616144250.431231566587-0.05274408474320.27408507774142.121250924519.5855849281-25.3163926407
53.31272777576-0.773394304276-2.132754649452.411392115420.9033333908616.866488998830.01583325283470.0817023077344-0.09888049175030.0607227574305-0.09126295829-0.2204148149290.561632322603-0.1817388390220.06651646072660.320742453663-0.0144412777353-0.04827368693710.293011705671-0.0111751647450.2640011711820.97945633214.82479240836-45.3895554097
64.568556530570.295636203744-0.7697905848227.04025361674-2.410454642976.11369453937-0.0983951612760.07448303562990.3118962326190.03152978082490.07876290277320.122359877243-0.3163281033610.3359102107060.01186941912580.21567590118-0.02655789172440.03483980282430.29553179726-0.04206899907070.2375256672428.992162365216.4690970215-77.0023945163
72.12719298762-1.288704198780.6638078867191.73067918626-0.2555485364195.425324630910.1796767511130.4171017178970.12563837846-0.178170698378-0.203999037972-0.0630222849234-0.0941871984696-0.3173224837060.002446055800130.263912037085-0.0003696424400440.00175945329590.5296246020030.005269957178930.2896708018782.228003333117.4801145194-49.9759704667
85.64390537851-1.45789680249-0.2789024333734.03202063781.394336136766.942132485040.1918850592930.410231714734-0.0203922100362-0.1561005415450.1110442594020.0494096257301-0.00300812607165-0.190552865136-0.2814173755270.29769449152-0.01951919872940.01486893525430.2413690009760.04533255541930.28440195528216.04291623411.9976039031-86.0003784979
91.716608149150.831068899285-1.343610977522.3332164566-1.446381011876.708029582760.09795830617980.06843534164810.0433370568531-0.0510374599442-0.0705882849460.2729040477110.434627325399-0.0226337301355-0.02671861610730.2792526410370.0481212580672-0.07798255140080.420576565788-0.03646259703750.32971728888727.82145255114.7574439300744.2534768877
108.709583271642.04817090461-0.6993262749696.18308857369-0.3603519930932.72416930083-0.1542014938750.08818939912690.0449821862774-0.0312973347019-0.06400737295390.08863703610230.0469134764431-0.4559419640840.2140046550570.318605758944-0.0002108701757590.07256360372130.468283574869-0.01984786137420.32280527819520.081381120817.147553997176.0501555853
111.541376627211.013058528160.6872528948762.04212850610.8316158576776.043442326480.1641928548290.02138231049160.04241999895940.0614255564465-0.0865723847360.0550920119629-0.1063455930110.136620339253-0.07402024248250.2509636044930.0554440146006-0.01408108604770.410344022134-0.0325503121240.27083638407546.934157461116.842916235848.2067225602
124.328752695842.33381803455-1.326616156054.83116682886-1.302653669784.890278578110.289236183923-0.825442082682-0.7923529288580.497229144644-0.562944340202-0.4785593808310.2224493506130.2901967895490.2755032166050.410845858246-0.0255414738734-0.008709380487010.6293718076720.136885881360.50016217015133.218753650712.231770005684.0991419055
130.2945687501040.1417581789-0.5711024891210.9938783129721.809218278583.8322619687-0.01313436653540.1029605770430.113941962002-0.0501287256239-0.004733571357330.0845028958001-0.193391657759-0.558558010190.009775854905270.3428504037030.098801351115-0.06241017417220.4254500980550.03853222394880.2711544498920.38804537865626.9726332623-13.7433109588
148.75817570336-2.29510411712.147992341062.63518109626-0.244528460463.6179059911-0.0102238569978-0.0114588606630.481865279826-0.104301790978-0.00313136486774-0.271360390302-0.3222184384870.04555947775760.05800565852540.278003945058-0.00828563095290.01803154108120.2026794430460.01012675554070.218539537112.577063327430.932645906114.4914308457
152.282398577610.07729079767092.284683012081.68586002674-0.06779326105636.35889682569-0.0619145393922-0.03069793794610.00804034551044-0.06947261298280.001510320938450.04129075635320.171874125011-0.2750200202090.05799277827710.264772874343-0.0228465244963-0.00699717262360.208384799561-0.02693123738540.233676186119.562778936285.826196677-12.3832844719
163.43151257552-2.78554120193-2.028168367893.232838065562.912552593433.10663348383-0.112264646674-0.228875198989-0.2543032390280.1510753408420.08106472903260.098168551850.1556473547180.01907266081350.02674955154860.2843741682660.0128449593944-0.03264950065520.2084166417430.03761698900820.2294081361836.8666840665618.968536275624.1881657364
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resid 1:124)AA1 - 1241 - 125
22(chain A and resid 125:227)AA125 - 227126 - 209
33(chain B and resid 1:107)BB1 - 1071 - 112
44(chain B and resid 108:213)BB108 - 213113 - 218
55(chain C and resid 1:116)CC1 - 1161 - 117
66(chain C and resid 117:227)CC117 - 227118 - 209
77(chain D and resid 1:107)DD1 - 1071 - 112
88(chain D and resid 108:213)DD108 - 213113 - 218
99(chain E and resid 1:116)EE1 - 1161 - 117
1010(chain E and resid 117:227)EE117 - 227118 - 211
1111(chain F and resid 1:104)FF1 - 1041 - 109
1212(chain F and resid 105:213)FF105 - 213110 - 218
1313(chain H and resid 1:126)HG1 - 1261 - 127
1414(chain H and resid 134:227)HG134 - 227128 - 209
1515(chain L and resid 1:107)LH1 - 1071 - 114
1616(chain L and resid 108:213)LH108 - 213115 - 220

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