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- PDB-8oyy: De novo designed soluble GPCR-like fold GLF_32 -

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Basic information

Entry
Database: PDB / ID: 8oyy
TitleDe novo designed soluble GPCR-like fold GLF_32
ComponentsDe novo designed soluble GPCR-like protein
KeywordsDE NOVO PROTEIN / GPCR / solubilized / de novo designed
Function / homology:
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 1.1Mar 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

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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)55,7298
Polymers55,5022
Non-polymers2276
Water3,657203
1
A: De novo designed soluble GPCR-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9045
Polymers27,7511
Non-polymers1534
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)27,8263
Polymers27,7511
Non-polymers752
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.278, 56.783, 202.974
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 or resid 3 through 8...
d_2ens_1(chain "B" and (resid 1 or resid 3 through 8...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLYGLYA2
d_12ens_1METLYSA4 - 9
d_13ens_1ALATYRA11 - 39
d_14ens_1ALALYSA41 - 43
d_15ens_1METGLYA45 - 97
d_16ens_1GLNGLYA99 - 145
d_17ens_1ARGARGA147 - 154
d_18ens_1LEUGLUA156 - 165
d_19ens_1TYRALAA167 - 177
d_110ens_1GLYALAA179 - 184
d_111ens_1ARGALAA186 - 216
d_112ens_1ALAGLUA218 - 233
d_21ens_1GLYGLYE1
d_22ens_1METLYSE3 - 8
d_23ens_1ALATYRE10 - 38
d_24ens_1ALALYSE40 - 42
d_25ens_1METGLYE44 - 96
d_26ens_1GLNGLYE98 - 144
d_27ens_1ARGARGE146 - 153
d_28ens_1LEUGLUE155 - 164
d_29ens_1TYRALAE166 - 176
d_210ens_1GLYALAE178 - 183
d_211ens_1ARGALAE185 - 215
d_212ens_1ALAGLUE217 - 232

NCS oper: (Code: givenMatrix: (0.999632496169, 0.0255408496442, 0.00908502081105), (-0.026326527165, 0.994570533829, 0.100679527249), (-0.00646425333017, -0.100881704185, 0.994877427219)Vector: 0. ...NCS oper: (Code: given
Matrix: (0.999632496169, 0.0255408496442, 0.00908502081105), (-0.026326527165, 0.994570533829, 0.100679527249), (-0.00646425333017, -0.100881704185, 0.994877427219)
Vector: 0.107466965085, -21.075226012, 35.9445637791)

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Components

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


Mass: 27750.949 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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.68 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M Na Acet pH 5.5, 0.2 M KBr, 25% PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.85→54.68 Å / Num. obs: 38883 / % possible obs: 97.65 % / Redundancy: 11.6 % / Biso Wilson estimate: 31 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.09567 / Net I/σ(I): 15.44
Reflection shellResolution: 1.852→1.918 Å / Redundancy: 11.6 % / Rmerge(I) obs: 1.526 / Mean I/σ(I) obs: 1.66 / Num. unique obs: 3930 / CC1/2: 0.78 / % possible all: 99.82

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→54.68 Å / SU ML: 0.2473 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.2974
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2379 1879 4.83 %
Rwork0.1936 37004 -
obs0.1958 38883 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.16 Å2
Refinement stepCycle: LAST / Resolution: 1.85→54.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3736 0 6 203 3945
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00633791
X-RAY DIFFRACTIONf_angle_d0.74535083
X-RAY DIFFRACTIONf_chiral_restr0.0429576
X-RAY DIFFRACTIONf_plane_restr0.0072658
X-RAY DIFFRACTIONf_dihedral_angle_d13.76411537
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.738557522283 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.31881460.27662871X-RAY DIFFRACTION99.83
1.9-1.960.33151190.26742893X-RAY DIFFRACTION99.87
1.96-2.020.27351530.24942852X-RAY DIFFRACTION100
2.02-2.090.28031290.2212882X-RAY DIFFRACTION99.9
2.09-2.180.25321530.20142881X-RAY DIFFRACTION99.97
2.18-2.280.2531470.19032844X-RAY DIFFRACTION99.93
2.28-2.40.28751560.20562873X-RAY DIFFRACTION99.97
2.4-2.550.27931480.21092890X-RAY DIFFRACTION100
2.55-2.740.23881420.20192676X-RAY DIFFRACTION92.15
2.74-3.020.2461490.20022956X-RAY DIFFRACTION100
3.02-3.460.23061340.19862650X-RAY DIFFRACTION90.71
3.46-4.350.21251460.16232611X-RAY DIFFRACTION87.94
4.35-54.680.2011570.17523125X-RAY DIFFRACTION99.64

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