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Basic information

Entry
Database: PDB / ID: 7udx
TitleDesigned pentameric proton channel QLQL
ComponentsDe novo designed pentameric proton channel QLQL
KeywordsMEMBRANE PROTEIN / Proton transport / de novo designed / pentameric
Function / homology(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsKratochvil, H.T. / Thomaston, J.L. / Liu, L. / DeGrado, W.F.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM138753 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122603 United States
National Science Foundation (NSF, United States)CHE1709506 United States
Air Force Office of Scientific ResearchFA9550-19-1-0331 United States
CitationJournal: Nat.Chem. / Year: 2023
Title: Transient water wires mediate selective proton transport in designed channel proteins.
Authors: Kratochvil, H.T. / Watkins, L.C. / Mravic, M. / Thomaston, J.L. / Nicoludis, J.M. / Somberg, N.H. / Liu, L. / Hong, M. / Voth, G.A. / DeGrado, W.F.
History
DepositionMar 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: 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
Revision 1.2Jul 19, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: De novo designed pentameric proton channel QLQL
B: De novo designed pentameric proton channel QLQL
C: De novo designed pentameric proton channel QLQL
D: De novo designed pentameric proton channel QLQL
E: De novo designed pentameric proton channel QLQL
F: De novo designed pentameric proton channel QLQL
G: De novo designed pentameric proton channel QLQL
H: De novo designed pentameric proton channel QLQL
I: De novo designed pentameric proton channel QLQL
J: De novo designed pentameric proton channel QLQL
K: De novo designed pentameric proton channel QLQL
L: De novo designed pentameric proton channel QLQL
M: De novo designed pentameric proton channel QLQL
N: De novo designed pentameric proton channel QLQL
O: De novo designed pentameric proton channel QLQL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,26916
Polymers45,91215
Non-polymers3571
Water1086
1
A: De novo designed pentameric proton channel QLQL
B: De novo designed pentameric proton channel QLQL
C: De novo designed pentameric proton channel QLQL
D: De novo designed pentameric proton channel QLQL
E: De novo designed pentameric proton channel QLQL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6616
Polymers15,3045
Non-polymers3571
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-75 kcal/mol
Surface area7480 Å2
MethodPISA
2
F: De novo designed pentameric proton channel QLQL
G: De novo designed pentameric proton channel QLQL
H: De novo designed pentameric proton channel QLQL
I: De novo designed pentameric proton channel QLQL
J: De novo designed pentameric proton channel QLQL


Theoretical massNumber of molelcules
Total (without water)15,3045
Polymers15,3045
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-73 kcal/mol
Surface area7360 Å2
MethodPISA
3
K: De novo designed pentameric proton channel QLQL
L: De novo designed pentameric proton channel QLQL
M: De novo designed pentameric proton channel QLQL
N: De novo designed pentameric proton channel QLQL
O: De novo designed pentameric proton channel QLQL


Theoretical massNumber of molelcules
Total (without water)15,3045
Polymers15,3045
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-74 kcal/mol
Surface area7670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.720, 83.680, 147.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein/peptide
De novo designed pentameric proton channel QLQL


Mass: 3060.801 Da / Num. of mol.: 15 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 1.87 Å3/Da / Density % sol: 34.1 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase
Details: 0.2 M ammonium sulfate, 0.1 M sodium chloride, 0.1 M sodium citrate, pH 6.0, 20% w/v PEG2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115832 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115832 Å / Relative weight: 1
ReflectionResolution: 2.99→73.51 Å / Num. obs: 7234 / % possible obs: 99.9 % / Redundancy: 13.1 % / Biso Wilson estimate: 64.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.145 / Net I/σ(I): 13.4
Reflection shellResolution: 2.99→3.04 Å / Num. unique obs: 348 / CC1/2: 0.921

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6MCT

6mct


Resolution: 2.99→73.51 Å / SU ML: 0.3719 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1179
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2728 723 9.99 %
Rwork0.2311 6511 -
obs0.2353 7234 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.79 Å2
Refinement stepCycle: LAST / Resolution: 2.99→73.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3077 0 14 6 3097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00263170
X-RAY DIFFRACTIONf_angle_d0.49024313
X-RAY DIFFRACTIONf_chiral_restr0.0322584
X-RAY DIFFRACTIONf_plane_restr0.0029466
X-RAY DIFFRACTIONf_dihedral_angle_d14.70551053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.220.30451420.26591279X-RAY DIFFRACTION99.79
3.22-3.540.3281410.26021275X-RAY DIFFRACTION100
3.55-4.060.31191450.24221290X-RAY DIFFRACTION99.72
4.06-5.110.2381450.20091303X-RAY DIFFRACTION99.79
5.11-73.510.24991500.23131364X-RAY DIFFRACTION99.08
Refinement TLS params.Method: refined / Origin x: -29.0003748753 Å / Origin y: -19.9591525395 Å / Origin z: 15.7630886382 Å
111213212223313233
T0.530404616609 Å20.0149911753246 Å20.0114580187153 Å2-0.360155892026 Å2-0.00115660193772 Å2--0.569932136997 Å2
L1.09943290131 °20.172884337277 °20.00848413877759 °2-0.0531121427929 °2-0.00824327851259 °2--1.66724933902 °2
S0.039658463518 Å °-0.0205613263611 Å °-0.0154938093129 Å °0.0392750564138 Å °0.00348568536453 Å °0.0043600075 Å °-0.0254577210218 Å °0.0859417251689 Å °-0.021205212318 Å °
Refinement TLS groupSelection details: chain A or chain B or chain C or chain D or chain E or chain F or chain G or chain H or chain I or chain J or chain K or chain L or chain M or chain N or chain O

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