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- PDB-8oyv: De novo designed Claudin fold CLF_4 -

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Basic information

Entry
Database: PDB / ID: 8oyv
TitleDe novo designed Claudin fold CLF_4
ComponentsDe novo designed soluble Claudin
KeywordsDE NOVO PROTEIN / claudin / solubilized / de novo designed
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 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

Downloads & links

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Assembly

Deposited unit
A: De novo designed soluble Claudin
B: De novo designed soluble Claudin


Theoretical massNumber of molelcules
Total (without water)45,4212
Polymers45,4212
Non-polymers00
Water181
1
A: De novo designed soluble Claudin


Theoretical massNumber of molelcules
Total (without water)22,7111
Polymers22,7111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: De novo designed soluble Claudin


Theoretical massNumber of molelcules
Total (without water)22,7111
Polymers22,7111
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.560, 50.770, 54.930
Angle α, β, γ (deg.)107.610, 90.490, 90.060
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 2 through 101 or resid 108 through 186))
d_2ens_1chain "B"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLUASNA2 - 101
d_12ens_1SERGLYA103 - 181
d_21ens_1GLUGLYB1 - 179

NCS oper: (Code: givenMatrix: (0.999966831339, 0.000295780047617, 0.00813933265649), (0.000317636741611, -0.9999963472, -0.00268415603045), (0.00813850900534, 0.00268665235169, -0.999963272611)Vector: ...NCS oper: (Code: given
Matrix: (0.999966831339, 0.000295780047617, 0.00813933265649), (0.000317636741611, -0.9999963472, -0.00268415603045), (0.00813850900534, 0.00268665235169, -0.999963272611)
Vector: -17.6814855045, -3.03858385237, 28.7760689496)

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Components

#1: Protein De novo designed soluble Claudin


Mass: 22710.654 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 2.08 Å3/Da / Density % sol: 40.89 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M sodium citrate pH 5, 0.1 M Sodium/Potassium phosphate pH 5.5, 0.1M Rubidium Chloride, 25% v/v PEG smear medium

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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: Apr 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.79→52.35 Å / Num. obs: 8007 / % possible obs: 88.03 % / Redundancy: 2.5 % / Biso Wilson estimate: 77.62 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1069 / Net I/σ(I): 6.34
Reflection shellResolution: 2.795→2.895 Å / Redundancy: 2.7 % / Rmerge(I) obs: 1.588 / Mean I/σ(I) obs: 1.42 / Num. unique obs: 858 / CC1/2: 0.437 / % possible all: 95.12

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→52.35 Å / SU ML: 0.458 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 42.9096
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3176 367 4.6 %
Rwork0.2725 7614 -
obs0.2744 7981 88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 97.64 Å2
Refinement stepCycle: LAST / Resolution: 2.79→52.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2950 0 0 1 2951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212978
X-RAY DIFFRACTIONf_angle_d0.47713992
X-RAY DIFFRACTIONf_chiral_restr0.0364460
X-RAY DIFFRACTIONf_plane_restr0.0036508
X-RAY DIFFRACTIONf_dihedral_angle_d13.33211206
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.423568396936 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.79-3.20.44281530.39662738X-RAY DIFFRACTION95.76
3.2-4.030.4034950.3292158X-RAY DIFFRACTION74.78
4.03-52.350.26111190.2312718X-RAY DIFFRACTION93.45

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