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- PDB-6dg6: Structure of a de novo designed Interleukin-2/Interleukin-15 mimetic -

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Basic information

Entry
Database: PDB / ID: 6dg6
TitleStructure of a de novo designed Interleukin-2/Interleukin-15 mimetic
ComponentsNeoleukin-2/15
KeywordsBIOSYNTHETIC PROTEIN / cytokine mimetic
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.999 Å
AuthorsJude, K.M. / Silva, D.-A. / Yu, S. / Baker, D. / Garcia, K.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1-AI51321 United States
CitationJournal: Nature / Year: 2019
Title: De novo design of potent and selective mimics of IL-2 and IL-15.
Authors: Silva, D.A. / Yu, S. / Ulge, U.Y. / Spangler, J.B. / Jude, K.M. / Labao-Almeida, C. / Ali, L.R. / Quijano-Rubio, A. / Ruterbusch, M. / Leung, I. / Biary, T. / Crowley, S.J. / Marcos, E. / ...Authors: Silva, D.A. / Yu, S. / Ulge, U.Y. / Spangler, J.B. / Jude, K.M. / Labao-Almeida, C. / Ali, L.R. / Quijano-Rubio, A. / Ruterbusch, M. / Leung, I. / Biary, T. / Crowley, S.J. / Marcos, E. / Walkey, C.D. / Weitzner, B.D. / Pardo-Avila, F. / Castellanos, J. / Carter, L. / Stewart, L. / Riddell, S.R. / Pepper, M. / Bernardes, G.J.L. / Dougan, M. / Garcia, K.C. / Baker, D.
History
DepositionMay 16, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neoleukin-2/15
B: Neoleukin-2/15
C: Neoleukin-2/15
D: Neoleukin-2/15
E: Neoleukin-2/15
F: Neoleukin-2/15


Theoretical massNumber of molelcules
Total (without water)72,6776
Polymers72,6776
Non-polymers00
Water1,00956
1
A: Neoleukin-2/15


Theoretical massNumber of molelcules
Total (without water)12,1131
Polymers12,1131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neoleukin-2/15


Theoretical massNumber of molelcules
Total (without water)12,1131
Polymers12,1131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Neoleukin-2/15


Theoretical massNumber of molelcules
Total (without water)12,1131
Polymers12,1131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Neoleukin-2/15


Theoretical massNumber of molelcules
Total (without water)12,1131
Polymers12,1131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Neoleukin-2/15


Theoretical massNumber of molelcules
Total (without water)12,1131
Polymers12,1131
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Neoleukin-2/15


Theoretical massNumber of molelcules
Total (without water)12,1131
Polymers12,1131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.730, 86.800, 92.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 or (resid 2 through 4...
21(chain B and (resid 1 through 5 or resid 7...
31(chain C and (resid 1 through 2 or (resid 3...
41(chain D and (resid 1 through 2 or (resid 3...
51(chain E and (resid 1 or (resid 2 through 4...
61(chain F and (resid 1 through 3 or (resid 4...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 or (resid 2 through 4...A1
121(chain A and (resid 1 or (resid 2 through 4...A2 - 4
131(chain A and (resid 1 or (resid 2 through 4...A1 - 100
141(chain A and (resid 1 or (resid 2 through 4...A1 - 100
151(chain A and (resid 1 or (resid 2 through 4...A1 - 100
161(chain A and (resid 1 or (resid 2 through 4...A1 - 100
211(chain B and (resid 1 through 5 or resid 7...B1 - 5
221(chain B and (resid 1 through 5 or resid 7...B7 - 20
231(chain B and (resid 1 through 5 or resid 7...B0
241(chain B and (resid 1 through 5 or resid 7...B24
251(chain B and (resid 1 through 5 or resid 7...B1 - 100
261(chain B and (resid 1 through 5 or resid 7...B1 - 100
271(chain B and (resid 1 through 5 or resid 7...B1 - 100
281(chain B and (resid 1 through 5 or resid 7...B1 - 100
311(chain C and (resid 1 through 2 or (resid 3...C1 - 2
321(chain C and (resid 1 through 2 or (resid 3...C3 - 4
331(chain C and (resid 1 through 2 or (resid 3...C-2 - 100
341(chain C and (resid 1 through 2 or (resid 3...C-2 - 100
351(chain C and (resid 1 through 2 or (resid 3...C-2 - 100
361(chain C and (resid 1 through 2 or (resid 3...C-2 - 100
411(chain D and (resid 1 through 2 or (resid 3...D1 - 2
421(chain D and (resid 1 through 2 or (resid 3...D3 - 4
431(chain D and (resid 1 through 2 or (resid 3...D-1 - 100
511(chain E and (resid 1 or (resid 2 through 4...E1
521(chain E and (resid 1 or (resid 2 through 4...E2 - 4
531(chain E and (resid 1 or (resid 2 through 4...E1 - 100
541(chain E and (resid 1 or (resid 2 through 4...E1 - 100
551(chain E and (resid 1 or (resid 2 through 4...E1 - 100
611(chain F and (resid 1 through 3 or (resid 4...F1 - 3
621(chain F and (resid 1 through 3 or (resid 4...F4
631(chain F and (resid 1 through 3 or (resid 4...F1 - 100
641(chain F and (resid 1 through 3 or (resid 4...F1 - 100
651(chain F and (resid 1 through 3 or (resid 4...F1 - 100
661(chain F and (resid 1 through 3 or (resid 4...F1 - 100

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Components

#1: Protein
Neoleukin-2/15


Mass: 12112.838 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.03 Å3/Da / Density % sol: 39.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4 M sodium malonate pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.999→39.276 Å / Num. obs: 40725 / % possible obs: 99.6 % / Redundancy: 8.643 % / Biso Wilson estimate: 34.54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.109 / Χ2: 1.018 / Net I/σ(I): 12.17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.999-2.058.1351.7811.2229180.5441.998.1
2.05-2.118.6741.3251.728930.6821.40899.8
2.11-2.179.020.9872.3528090.821.04699.9
2.17-2.238.9970.7932.8427730.8780.8499.8
2.23-2.318.9040.6683.3626450.9080.709100
2.31-2.398.7290.5284.1625600.9360.561100
2.39-2.488.2530.3865.3724960.9540.41299.4
2.48-2.588.6660.3376.3624090.9720.35899.9
2.58-2.699.070.277.9722980.980.28699.9
2.69-2.838.9410.20610.1422140.9870.218100
2.83-2.988.8230.1513.5920930.9920.159100
2.98-3.168.6120.12415.8220010.9930.13299.8
3.16-3.388.2460.08820.1718790.9960.09499.7
3.38-3.659.0320.06927.117680.9970.073100
3.65-48.7660.05731.4716260.9980.061100
4-4.478.4550.0534.0714790.9980.05399.7
4.47-5.167.9460.04735.1113030.9990.05198.6
5.16-6.328.5630.05432.0711370.9980.058100
6.32-8.947.7910.04137.478910.9990.04499.9
8.94-39.2767.310.03738.685330.9990.0496.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.61 Å48 Å
Translation2.61 Å48 Å

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Processing

Software
NameVersionClassification
XDS20170601data reduction
XSCALE20170601data scaling
PHASER2.7.16phasing
PHENIX1.13-2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: predicted model

Resolution: 1.999→39.276 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.49
RfactorNum. reflection% reflection
Rfree0.2261 1841 4.88 %
Rwork0.2038 --
obs0.205 37755 92.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 149.56 Å2 / Biso mean: 52.6098 Å2 / Biso min: 19.99 Å2
Refinement stepCycle: final / Resolution: 1.999→39.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4705 0 0 56 4761
Biso mean---54.21 -
Num. residues----597
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2048X-RAY DIFFRACTION11.093TORSIONAL
12B2048X-RAY DIFFRACTION11.093TORSIONAL
13C2048X-RAY DIFFRACTION11.093TORSIONAL
14D2048X-RAY DIFFRACTION11.093TORSIONAL
15E2048X-RAY DIFFRACTION11.093TORSIONAL
16F2048X-RAY DIFFRACTION11.093TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9985-2.05260.34411170.31882246236377
2.0526-2.1130.30981030.27382443254682
2.113-2.18120.26321390.24012503264286
2.1812-2.25910.27591380.23422618275689
2.2591-2.34950.26651440.23122675281991
2.3495-2.45650.26521400.21482745288593
2.4565-2.5860.23761400.21012815295595
2.586-2.74790.25181470.21232852299996
2.7479-2.960.26071500.20952912306298
2.96-3.25780.26691570.22292941309899
3.2578-3.72890.21781500.200129963146100
3.7289-4.69680.16141560.1653022317899
4.6968-39.28330.21541600.19583146330699
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)
13.0321-0.72780.19791.7981-0.26292.52060.04060.2608-0.1753-0.22360.04460.08240.11790.0964-0.0860.2956-0.0091-0.05620.2804-0.06550.413714.847445.8485-21.6651
20.9371-0.9452-0.37552.5936-1.27612.01980.0918-0.1381-0.54730.1286-0.20110.06460.3837-0.11580.35190.4063-0.1291-0.03810.37090.00530.56329.293739.8265-14.1087
30.4958-0.0511-0.5420.33390.21650.5975-0.1478-0.38460.5147-0.2368-0.20460.68610.055-0.71090.13030.3315-0.0075-0.06460.4065-0.10960.48677.723950.0973-15.6104
43.6174-0.76321.88681.4982-0.47363.08310.8827-0.0451-0.3918-0.4217-0.108-0.41010.10350.5340.20530.663-0.10520.16040.3106-0.05810.371424.8403103.08049.7203
50.9598-0.27180.0351.7768-0.63970.29160.21310.1181-0.4428-0.68070.1947-0.3307-0.09010.4751-0.06870.9107-0.03330.21580.3311-0.0230.376525.387199.23170.4873
60.63140.20380.3060.5499-0.58260.7764-0.16550.47290.3741-0.44630.0003-0.04840.05450.4498-0.33491.1056-0.0770.87130.29090.44740.42228.9443107.1495-3.5903
72.38490.1912-0.00650.79380.11891.64110.2618-0.03180.7651-0.1329-0.0192-0.6661-0.36890.71590.04061.0057-0.16930.350.2817-0.03730.711528.9871110.89846.1843
83.21730.59490.97983.7070.64260.85780.28050.3633-0.41670.0998-0.04630.3265-0.2266-0.0054-0.00710.39090.00550.01120.34050.00040.43711.8921122.193118.4256
91.3547-0.76170.34931.68150.39292.10640.12030.2847-0.1194-0.4679-0.27820.3984-0.3091-0.73020.11330.47480.063-0.05230.4359-0.01560.4714.5205125.118115.2863
106.8461-2.0465-0.9612.80890.8472.44830.1937-0.19740.4358-0.1079-0.0077-0.1378-0.23320.0131-0.24920.437-0.08710.05370.3025-0.01210.206614.094397.243413.8691
113.6241-2.51660.99945.0666-0.55111.81620.38580.2058-0.119-0.7974-0.42530.2467-0.4531-0.00020.05530.46410.0017-0.03370.3456-0.06560.314711.287192.04677.164
121.19450.1355-0.32882.50551.13331.60320.0701-0.3333-0.31510.1103-0.01510.41550.1211-0.0601-0.07920.3928-0.07330.02460.38170.01480.35128.847788.379916.444
134.4032-1.19140.56393.09320.54093.35670.0152-0.3431-0.11580.14150.15940.1555-0.2013-0.2275-0.02570.1803-0.0362-0.01350.2773-0.03440.1993-10.561130.726-33.805
143.2664-0.5311-3.13313.40083.32835.50660.086-0.6977-0.26970.5548-0.4859-0.25350.58590.22190.33520.5428-0.0821-0.08730.52070.05930.7489-1.389215.6999-35.0519
151.8815-1.2522-0.20246.58410.81281.87950.1110.3517-0.0593-0.9195-0.2642-0.1211-0.27780.16660.1260.3179-0.07270.00840.3582-0.04710.3053-6.657136.2491-41.4614
163.7812-2.77971.01117.0072-0.79672.0715-0.10930.1510.2411-0.36530.2472-1.0381-0.48450.44-0.16710.3766-0.10220.02080.421-0.10650.4709-0.642240.748-36.4134
173.9142-0.1823-0.77753.8020.08964.2675-0.2599-0.5012-0.03270.29240.4172-0.8647-0.01860.5988-0.17540.2588-0.0517-0.0450.3354-0.07770.3279-2.967434.1043-28.623
181.903-0.82040.46732.3243-0.25382.713-0.0416-0.0908-0.12480.106-0.0259-0.0046-0.23390.00680.06340.16640.0258-0.02710.28170.02040.228719.411769.5889-2.5435
194.05061.2024-2.62230.7964-1.34463.5525-0.0426-0.4993-0.4280.2151-0.2701-0.2372-0.11870.40730.22110.2454-0.0195-0.11350.39640.08490.360826.024266.1455.2715
204.63071.51940.04353.7213-0.00272.7379-0.2327-0.0095-0.4859-0.1765-0.0093-0.97620.0170.3980.130.22390.0367-0.05620.3505-0.02330.42928.502764.2222-5.0899
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 1 through 54 )D1 - 54
2X-RAY DIFFRACTION2chain 'D' and (resid 55 through 76 )D55 - 76
3X-RAY DIFFRACTION3chain 'D' and (resid 77 through 100 )D77 - 100
4X-RAY DIFFRACTION4chain 'E' and (resid 2 through 30 )E2 - 30
5X-RAY DIFFRACTION5chain 'E' and (resid 31 through 55 )E31 - 55
6X-RAY DIFFRACTION6chain 'E' and (resid 56 through 76 )E56 - 76
7X-RAY DIFFRACTION7chain 'E' and (resid 77 through 100 )E77 - 100
8X-RAY DIFFRACTION8chain 'F' and (resid 2 through 23 )F2 - 23
9X-RAY DIFFRACTION9chain 'F' and (resid 24 through 100 )F24 - 100
10X-RAY DIFFRACTION10chain 'A' and (resid 1 through 27 )A1 - 27
11X-RAY DIFFRACTION11chain 'A' and (resid 28 through 54 )A28 - 54
12X-RAY DIFFRACTION12chain 'A' and (resid 55 through 100 )A55 - 100
13X-RAY DIFFRACTION13chain 'B' and (resid 2 through 24 )B2 - 24
14X-RAY DIFFRACTION14chain 'B' and (resid 25 through 33 )B25 - 33
15X-RAY DIFFRACTION15chain 'B' and (resid 34 through 55 )B34 - 55
16X-RAY DIFFRACTION16chain 'B' and (resid 56 through 76 )B56 - 76
17X-RAY DIFFRACTION17chain 'B' and (resid 77 through 100 )B77 - 100
18X-RAY DIFFRACTION18chain 'C' and (resid -2 through 55 )C-2 - 55
19X-RAY DIFFRACTION19chain 'C' and (resid 56 through 76 )C56 - 76
20X-RAY DIFFRACTION20chain 'C' and (resid 77 through 100 )C77 - 100

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