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- PDB-7qt4: Antibody FenAb709 - fentanyl complex -

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Basic information

Entry
Database: PDB / ID: 7qt4
TitleAntibody FenAb709 - fentanyl complex
Components
  • Antibody heavy chain
  • Antibody light chain
KeywordsIMMUNE SYSTEM / Antibody
Function / homologyChem-FD0
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.32 Å
AuthorsZeelen, J.P. / Straaten van, M. / Stebbins, C.E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Rep / Year: 2023
Title: A trypanosome-derived immunotherapeutics platform elicits potent high-affinity antibodies, negating the effects of the synthetic opioid fentanyl.
Authors: Triller, G. / Vlachou, E.P. / Hashemi, H. / van Straaten, M. / Zeelen, J.P. / Kelemen, Y. / Baehr, C. / Marker, C.L. / Ruf, S. / Svirina, A. / Chandra, M. / Urban, K. / Gkeka, A. / Kruse, S. ...Authors: Triller, G. / Vlachou, E.P. / Hashemi, H. / van Straaten, M. / Zeelen, J.P. / Kelemen, Y. / Baehr, C. / Marker, C.L. / Ruf, S. / Svirina, A. / Chandra, M. / Urban, K. / Gkeka, A. / Kruse, S. / Baumann, A. / Miller, A.K. / Bartel, M. / Pravetoni, M. / Stebbins, C.E. / Papavasiliou, F.N. / Verdi, J.P.
History
DepositionJan 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antibody heavy chain
B: Antibody light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4153
Polymers47,7972
Non-polymers6181
Water4,702261
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.190, 138.690, 101.070
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-505-

HOH

21A-507-

HOH

31B-327-

HOH

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Components

#1: Antibody Antibody heavy chain


Mass: 24079.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Freestyle 293F / Production host: Homo sapiens (human)
#2: Antibody Antibody light chain


Mass: 23717.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): Freestyle 293F / Production host: Homo sapiens (human)
#3: Chemical ChemComp-FD0 / 2-[2-[2-[2-[[5-oxidanylidene-5-[2-[4-[phenyl(propanoyl)amino]piperidin-1-yl]ethylamino]pentanoyl]amino]ethanoylamino]ethanoylamino]ethanoylamino]ethanoic acid


Mass: 617.694 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H43N7O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.76 Å3/Da / Density % sol: 55.38 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 40 % (V/V) MPD, 0.1 M Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.32→55.32 Å / Num. obs: 22297 / % possible obs: 94.77 % / Redundancy: 10.9 % / Biso Wilson estimate: 25.34 Å2 / CC1/2: 0.971 / Net I/σ(I): 16.19
Reflection shellResolution: 2.32→2.41 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.2856 / Mean I/σ(I) obs: 7.3 / Num. unique obs: 2274 / CC1/2: 0.978 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7QT0

7qt0


Resolution: 2.32→55.32 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2476 2106 5.03 %
Rwork0.2089 39723 -
obs0.2108 22297 94.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.92 Å2 / Biso mean: 32.4177 Å2 / Biso min: 7.61 Å2
Refinement stepCycle: final / Resolution: 2.32→55.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3180 0 28 261 3469
Biso mean--27.19 29.67 -
Num. residues----415
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.32-2.370.30562090.22682730100
2.37-2.430.26431680.22382744100
2.43-2.50.2731410.23682825100
2.5-2.570.26651450.22042793100
2.57-2.660.25211320.23582804100
2.66-2.750.28671160.23052837100
2.75-2.860.3261650.23852781100
2.86-2.990.23211370.2242812100
2.99-3.150.28711330.21992823100
3.15-3.350.28971480.2305274999
3.35-3.60.2398920.2116206573
3.6-3.970.2394660.2334142551
3.97-4.540.21091690.1645271698
4.54-5.720.19651340.15152832100
5.72-55.321510.21432787100
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)
11.96940.13340.09143.2993-0.83532.44490.09-0.15460.02850.3191-0.01890.01310.0016-0.0623-0.10760.10270.02950.01110.1580.0050.1574-3.60222.828-1.856
22.0717-0.26290.07332.2312-0.44752.56630.04870.07240.10470.04850.0280.10180.02270.0275-0.06780.08130.00410.02340.1229-0.01560.1218-4.4122.531-6.883
30.54140.34441.04911.0270.98932.1796-0.3517-0.61710.39350.76390.0455-0.1313-0.7728-0.56540.30780.8910.1989-0.23510.411-0.06120.348310.02712.83319.475
42.1447-0.16951.29971.6830.10162.6604-0.07120.1734-0.06630.0120.0662-0.2001-0.01590.23160.01090.1354-0.03140.00710.1590.00010.183217.62624.949-11.91
50.80320.33370.16780.3336-0.15331.40650.03790.1477-0.07880.269-0.1259-0.2629-0.08870.2020.06820.1851-0.028-0.08650.1253-0.00950.279317.50618.835-7.956
61.21451.5463-0.31033.909-3.08534.1476-0.2537-0.03660.13740.34790-0.2465-0.4749-0.30710.19360.420.0019-0.16230.2118-0.00340.339221.8482.36719.328
70.70430.3877-0.68354.6675-2.05961.2978-0.18190.10220.0650.49210.0427-0.1758-0.42620.07160.17490.4041-0.0064-0.14480.2345-0.0110.294321.8859.4198.927
83.80492.4001-2.10973.6533-2.78564.00090.0042-0.2427-0.24670.3408-0.4951-0.4062-0.39790.21670.46160.3128-0.0335-0.13910.20260.00930.381424.311-1.6422.176
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:43 )A2 - 43
2X-RAY DIFFRACTION2( CHAIN A AND RESID 44:117 )A44 - 117
3X-RAY DIFFRACTION3( CHAIN A AND RESID 118:218 )A118 - 218
4X-RAY DIFFRACTION4( CHAIN B AND RESID 1:90 )B1 - 90
5X-RAY DIFFRACTION5( CHAIN B AND RESID 91:113 )B91 - 113
6X-RAY DIFFRACTION6( CHAIN B AND RESID 114:155 )B114 - 155
7X-RAY DIFFRACTION7( CHAIN B AND RESID 156:174 )B156 - 174
8X-RAY DIFFRACTION8( CHAIN B AND RESID 175:211 )B175 - 211

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