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- PDB-8v9x: X-ray crystal structure of JGFN4 complex with fentanyl -

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Basic information

Entry
Database: PDB / ID: 8v9x
TitleX-ray crystal structure of JGFN4 complex with fentanyl
ComponentsJGFN4
KeywordsANTITOXIN
Function / homologyChem-7V7
Function and homology information
Biological speciesCamelidae (mammal)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMoller, N. / Shi, K. / Aihara, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01-CA214279 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37-AI064064 United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Identification and biophysical characterization of a novel domain-swapped camelid antibody specific for fentanyl.
Authors: Gallant, J.P. / Hicks, D. / Shi, K. / Moeller, N.H. / Hoppe, B. / Lake, E.W. / Baehr, C. / Pravetoni, M. / Aihara, H. / LeBeau, A.M.
History
DepositionDec 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: JGFN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3343
Polymers12,9351
Non-polymers3992
Water2,252125
1
A: JGFN4
hetero molecules

A: JGFN4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6686
Polymers25,8712
Non-polymers7974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area4600 Å2
ΔGint-18 kcal/mol
Surface area11420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.791, 109.067, 50.199
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

21A-409-

HOH

31A-418-

HOH

41A-425-

HOH

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Components

#1: Antibody JGFN4


Mass: 12935.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-7V7 / N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide


Mass: 336.471 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H28N2O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl, pH 8.0, 0.2 M LiCl, 20% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Apr 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.55→41.43 Å / Num. obs: 17841 / % possible obs: 98.1 % / Redundancy: 4.3 % / Biso Wilson estimate: 21.38 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.056 / Rrim(I) all: 0.124 / Net I/σ(I): 8.1 / Num. measured all: 75941
Reflection shellResolution: 1.55→1.58 Å / % possible obs: 90.8 % / Redundancy: 3.2 % / Rmerge(I) obs: 2.011 / Num. measured all: 2519 / Num. unique obs: 792 / CC1/2: 0.301 / Rpim(I) all: 1.199 / Rrim(I) all: 2.365 / Net I/σ(I) obs: 0.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→41.43 Å / SU ML: 0.2311 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.0151
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2181 861 4.84 %
Rwork0.1867 16937 -
obs0.1882 17798 97.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.82 Å2
Refinement stepCycle: LAST / Resolution: 1.55→41.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms846 0 29 125 1000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082911
X-RAY DIFFRACTIONf_angle_d0.95941224
X-RAY DIFFRACTIONf_chiral_restr0.062134
X-RAY DIFFRACTIONf_plane_restr0.0071157
X-RAY DIFFRACTIONf_dihedral_angle_d14.5707328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.650.35561340.34682667X-RAY DIFFRACTION93.77
1.65-1.770.36041570.29722786X-RAY DIFFRACTION98.4
1.77-1.950.27021330.2152845X-RAY DIFFRACTION98.58
1.95-2.240.2021480.18452838X-RAY DIFFRACTION98.74
2.24-2.820.21761530.17762861X-RAY DIFFRACTION98.5
2.82-41.430.18061360.15782940X-RAY DIFFRACTION96.55
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)
13.12122622274-2.348830190792.610078884138.75138998475-4.905128222133.444403636170.5032658559050.444230908995-0.254037370257-0.570432079904-0.755225325559-0.3124100236650.6028705205960.5730219851170.1074654442270.2808654699260.0245671312068-0.01027598619040.329717075506-0.006581422362610.263015176642-7.98389364192-30.5972087780.761533320591
25.95190374055-1.1528247463-1.871757727034.376279972176.396145828539.360641422150.1137227415220.03539233684040.155760368947-0.294730564193-0.337171468863-0.059027195652-0.678264682334-0.604879718580.1839790605270.3251864814710.0421592026746-0.06778762715860.2822800117150.06570478965510.260650500821-11.4427734497-7.39233883608-7.24587304826
30.01099054533750.2727505209380.2666630418772.016799298621.383215810989.075722949180.243850388230.06339452419170.0776162022211-0.202516916464-0.2523604832710.321607115625-0.1155842645110.2093331329510.01041901522750.137674433809-0.00747303415403-0.01412688375520.2458162864440.02079916944040.273258277038-12.557617253-21.45494157440.591046023704
46.412016813926.567630373126.160014883056.69152576776.276551642975.918074077580.269662348184-0.0416999042647-0.4729848820740.153847683801-0.210537138444-0.03867290948940.503472609558-0.0046836052737-0.1443760534960.265492356717-0.00428552200558-0.0211727479130.1840097667790.01218641908190.295200449358-8.61675865555-33.651503092311.7319538874
54.240721756286.02552318546-5.083568568198.49490639048-7.015376728325.903472619680.1529260059940.03103944742230.280575808063-0.05256235694670.02301794161250.292318817015-0.0947687564079-0.00256128826171-0.2652515312210.1771650171990.001501400525190.00913414758610.1785785901040.01354323354550.177147371048-2.89732350537-19.32809622813.19953544707
69.132549112251.28016768702-6.102978267682.97947035694-0.9304126697274.115307676290.3540764124850.1638044696490.448056479045-0.103467207851-0.0672502455636-0.0666207776141-0.5584982663310.399573915594-0.3317304000390.237758383347-0.0508170131801-0.01814354699140.3190718235220.01370006547280.1995564935131.9812108426-16.27924390822.70469852428
71.116961475581.2545866892-1.029891910995.10382247325-5.476472758147.343424676460.18651920383-0.2165822276840.0770920703350.380909871798-0.221138797284-0.0768085426119-0.5062650523250.227607990122-0.007094279006320.194365885369-0.009309286056670.0187282213590.209424999481-0.01661498142030.206947303351-7.25557411902-18.006424519414.9613442668
82.39097264399-1.73233477615-0.2402089575568.0848805758-4.025043728282.61058475548-0.544851320152-0.9058029993540.8850939479411.248597002390.134726771063-0.401106851248-1.077768730630.1270744361210.2293984851460.511247999451-0.053339156072-0.04896093771240.310679995806-0.03369533919630.23228708272-2.62888734494-6.478418109786.96519874179
93.801366712823.88183347772-0.9927678741477.28223659967-1.241785145062.457416363260.220030989845-0.2458154798550.08636790881620.074155542773-0.2084441585210.0222237187231-0.190671729825-0.0626412188132-0.0268552521320.1741853632810.0102644902066-0.006614723565550.2153057206990.009843639812640.204127948898-13.6683427055-19.11995506296.63980377724
101.59653664571-1.291257435190.9653930817235.28566500165-3.076740971185.350334744820.0451986519166-0.09164731090190.2217539384890.0683051697469-0.1383964876460.0703339899184-0.5275218234120.1885743064470.08422918874530.176595798953-0.0114092381188-0.0007784576871650.139717386246-0.0111295790580.15853174721-3.66350196383-13.586929793-1.27872199307
111.842372166362.647305656262.011660335423.901990451992.355584348596.305047093980.172053394765-0.2762471071930.08011535809030.14583353897-0.2473253261850.0673620858731-0.141785467402-0.1871127411290.08210610437250.1248662380340.03984545583230.01152480529130.212311937929-0.006984570324620.1906789354262.76585120514-19.609272340428.7765948507
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 8 )0 - 81 - 9
22chain 'A' and (resid 9 through 17 )9 - 1710 - 18
33chain 'A' and (resid 18 through 25 )18 - 2519 - 26
44chain 'A' and (resid 26 through 32 )26 - 3227 - 33
55chain 'A' and (resid 33 through 39 )33 - 3934 - 40
66chain 'A' and (resid 40 through 52 )40 - 5241 - 53
77chain 'A' and (resid 53 through 59 )53 - 5954 - 60
88chain 'A' and (resid 60 through 66 )60 - 6661 - 67
99chain 'A' and (resid 67 through 82 )67 - 8268 - 83
1010chain 'A' and (resid 83 through 98 )83 - 9884 - 99
1111chain 'A' and (resid 99 through 113 )99 - 113100 - 114

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