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- PDB-8oyx: De novo designed soluble GPCR-like fold GLF_18 -

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Basic information

Entry
Database: PDB / ID: 8oyx
TitleDe novo designed soluble GPCR-like fold GLF_18
ComponentsDe novo designed soluble GPCR-like protein
KeywordsDE NOVO PROTEIN / GPCR / solubilized / de novo designed
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsPacesa, M. / Correia, B.E.
Funding support Switzerland, European Union, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
European Research Council (ERC)716058European Union
CitationJournal: Biorxiv / Year: 2024
Title: Computational design of soluble functional analogues of integral membrane proteins.
Authors: Goverde, C.A. / Pacesa, M. / Goldbach, N. / Dornfeld, L.J. / Balbi, P.E.M. / Georgeon, S. / Rosset, S. / Kapoor, S. / Choudhury, J. / Dauparas, J. / Schellhaas, C. / Kozlov, S. / Baker, D. / ...Authors: Goverde, C.A. / Pacesa, M. / Goldbach, N. / Dornfeld, L.J. / Balbi, P.E.M. / Georgeon, S. / Rosset, S. / Kapoor, S. / Choudhury, J. / Dauparas, J. / Schellhaas, C. / Kozlov, S. / Baker, D. / Ovchinnikov, S. / Vecchio, A.J. / Correia, B.E.
History
DepositionMay 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Revision 1.2Mar 27, 2024Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: De novo designed soluble GPCR-like protein
B: De novo designed soluble GPCR-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6564
Polymers55,4662
Non-polymers1902
Water79344
1
A: De novo designed soluble GPCR-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8282
Polymers27,7331
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: De novo designed soluble GPCR-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8282
Polymers27,7331
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.726, 52.084, 58.392
Angle α, β, γ (deg.)94.080, 104.360, 110.800
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 2 or resid 4...
d_2ens_1(chain "B" and (resid 1 through 2 or resid 4...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYARGA1 - 2
d_12ens_1GLUGLUA4 - 18
d_13ens_1ALAGLUA20 - 65
d_14ens_1VALARGA67 - 98
d_15ens_1PROILEA106 - 112
d_16ens_1ALAALAA114 - 176
d_17ens_1ASNILEA178 - 194
d_18ens_1GLUALAA196 - 232
d_19ens_1PO4PO4B
d_21ens_1GLYARGC1 - 2
d_22ens_1GLUGLUC4 - 18
d_23ens_1ALAGLUC20 - 65
d_24ens_1VALILEC67 - 105
d_25ens_1ALAALAC107 - 169
d_26ens_1ASNILEC171 - 187
d_27ens_1GLUALAC189 - 225
d_28ens_1PO4PO4D

NCS oper: (Code: givenMatrix: (0.999052582918, -0.0068313051023, -0.0429798770902), (-0.00657714193963, -0.999960055414, 0.00605217146371), (-0.0430195045067, -0.00576375278091, -0.99905760664)Vector: ...NCS oper: (Code: given
Matrix: (0.999052582918, -0.0068313051023, -0.0429798770902), (-0.00657714193963, -0.999960055414, 0.00605217146371), (-0.0430195045067, -0.00576375278091, -0.99905760664)
Vector: -0.60424512891, -38.8545768267, -23.548558342)

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Components

#1: Protein De novo designed soluble GPCR-like protein


Mass: 27732.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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

Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: Na Phos Cit pH 4.2, 0.2 M LiSO4, 20% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.11→47.93 Å / Num. obs: 20309 / % possible obs: 88.48 % / Redundancy: 1.7 % / Biso Wilson estimate: 36.73 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.04953 / Net I/σ(I): 9.89
Reflection shellResolution: 2.11→2.185 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 3.35 / Num. unique obs: 2144 / CC1/2: 0.748 / % possible all: 92.81

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.11→47.93 Å / SU ML: 0.2782 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.55
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2507 1017 5.01 %
Rwork0.2025 19292 -
obs0.2049 20309 88.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.5 Å2
Refinement stepCycle: LAST / Resolution: 2.11→47.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3686 0 10 44 3740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00573739
X-RAY DIFFRACTIONf_angle_d0.87715045
X-RAY DIFFRACTIONf_chiral_restr0.0501588
X-RAY DIFFRACTIONf_plane_restr0.0078651
X-RAY DIFFRACTIONf_dihedral_angle_d5.663488
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.668379666205 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.220.32241470.25052864X-RAY DIFFRACTION91.97
2.22-2.350.26871520.23112816X-RAY DIFFRACTION90.08
2.35-2.540.26811720.22622723X-RAY DIFFRACTION88.97
2.54-2.790.30091350.21612751X-RAY DIFFRACTION87.99
2.79-3.20.26451190.22132670X-RAY DIFFRACTION84.9
3.2-4.030.25961550.18922658X-RAY DIFFRACTION85.79
4.03-47.930.20961370.18312810X-RAY DIFFRACTION89.82
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)
12.230767277880.6803222707021.03796582485.598677797343.006023837692.770540263050.0554965312235-0.75327324723-0.04402038953260.0464577136411-0.5933600897920.5888114853630.255077922464-1.557040643050.009501255187090.353211118481-0.09413727295980.04666775307650.5958425634960.03630201901920.4329789222-20.8391992734-7.7614045036-1.35216008227
21.759169759251.02866526349-2.412474207581.11877446486-2.225639921554.627650808690.9183332003970.715344789203-0.579740974715-1.879140803791.2777194472-0.1072455735831.33676943353-0.694339554798-0.06804580050921.02561004547-0.2962499454890.1211371004360.65285551844-0.08646349761340.783134141706-18.5194714064-16.6730761562-22.9823669968
33.974011729680.6921554518570.9789715186253.214731461620.4011924250498.07953751260.121420943257-0.449878973688-0.5871351190310.225585016142-0.0928337553743-0.08882957278831.695680138680.0980823796585-0.07510707993340.31762709697-0.0221383387739-0.1063780046640.2716940149110.09906617371750.448582568112-11.9239290756-11.7352801072-1.88122788079
42.489236500070.7146062139660.1063953719922.98438814580.4748470062552.619999014680.0801869606770.0248234053149-0.338653395064-0.2282639375110.1536835883810.01237467392990.7125337150240.199366450389-0.1656594535720.2517895328580.0492909902906-0.02044951607220.227844915071-0.03411093057090.402643708086-3.87523132338-9.47047976483-10.4441477132
53.31377507269-0.03879924452310.4384536284162.91314203207-0.04122609023826.639123713440.0489211930880.06521653687730.0958204870188-0.419498604626-0.224705217050.1495771846550.7178048452150.912353529243-0.04991174430560.3670139918820.0168088868509-0.03240106874370.315404996658-0.09946535048640.5636330065962.67724080644-14.104170396-12.8418474066
63.146447282620.124328961151-0.7550498568662.35079578472-0.6582044435085.335417197230.153151656978-0.1702159729590.149973679904-0.0796233225595-0.0429351326169-0.219761006254-0.3484869172570.282010673179-0.1662485357220.219804637981-0.04053551662590.02961054555280.18617017791-0.01224005983730.287188432192-1.408561647911.26921001678-6.6526037531
73.30371082572-0.2669133571412.221270006751.75994196519-0.0995732307967.080410429660.00832082033546-0.6297153799230.08557022958630.2099288248490.2325802650240.0571062364301-0.55086906908-0.484535596971-0.07511522057240.2512476040160.01423224019790.03273940052950.28320210853-0.000781631853410.206921708836-10.8906692166-0.1038913183972.38911964133
83.048556969270.3582414992613.778918921136.522908838940.01804657861074.70260451939-0.422894860750.25003886006-0.640868711026-1.466618553570.3732529273630.3773235693730.416638863026-0.710332184117-0.2715655676460.516213680772-0.105868091925-0.03969144824910.265132077418-0.04110103661970.335191114242-19.6779319846-5.31284776302-18.5759686228
93.55843031439-0.259019406766-0.7290048177056.09286996083.240558030313.304033136060.05083258487030.4871141996550.157678580029-0.276598126184-0.5706421926380.720254158706-0.449440351442-2.249721152650.6488944952940.388905870990.0581776448536-0.08147851101810.5574206928390.02908209713720.464693202015-21.2803540449-30.876894754-21.426738314
102.45024983642-0.2578489852521.299016603832.691065978560.4047400062184.60344057953-0.17602909163-0.03415631941180.2661901509440.400501748892-0.08059943551980.153659791151-0.471997095148-0.2375396604740.3812043706840.32993804097-0.002258820174730.0382409955770.1842990077320.005113903852420.351060815888-9.09642344238-27.372750877-16.2520933689
112.632541798640.755257727763-0.3980550526242.985130767750.05183522682524.375098918440.1251540856750.02768620842710.2294667206990.1354254788160.0604621931845-0.181719245495-0.1957696421590.598166250836-0.1188487375560.2382808491980.0326776657429-0.009593220015010.289763664052-0.02148938857460.3986528601542.7220074443-30.8392459712-15.2646867383
123.45904315106-0.3959941811150.4339059822692.93079469752-0.7140385938763.18960938333-0.0323674072642-0.167129735825-0.455722797250.1757211131170.03136321574110.1460905441470.3772374493430.06280535884070.01470072937810.24839200904-0.0145904797819-0.01081948096670.2222561091820.01658258503170.258851121967-10.0767179529-40.1795047644-16.75249965
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 26 )AA1 - 261 - 26
22chain 'A' and (resid 27 through 35 )AA27 - 3527 - 35
33chain 'A' and (resid 36 through 63 )AA36 - 6336 - 63
44chain 'A' and (resid 64 through 101 )AA64 - 10164 - 101
55chain 'A' and (resid 102 through 136 )AA102 - 136102 - 136
66chain 'A' and (resid 137 through 199 )AA137 - 199137 - 199
77chain 'A' and (resid 200 through 221 )AA200 - 221200 - 221
88chain 'A' and (resid 222 through 232 )AA222 - 232222 - 232
99chain 'B' and (resid 1 through 26 )BC1 - 261 - 26
1010chain 'B' and (resid 27 through 97 )BC27 - 9727 - 97
1111chain 'B' and (resid 98 through 169 )BC98 - 16998 - 162
1212chain 'B' and (resid 170 through 232 )BC170 - 232163 - 225

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