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Basic information

Entry
Database: PDB / ID: 7udw
TitleDesigned pentameric proton channel QQLL
ComponentsDe novo designed pentameric proton channel QQLL
KeywordsMEMBRANE PROTEIN / Proton transport / de novo designed / pentameric
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKratochvil, H.T. / Thomaston, J.L. / Mravic, M. / Nicoludis, J. / 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 QQLL
B: De novo designed pentameric proton channel QQLL
C: De novo designed pentameric proton channel QQLL
D: De novo designed pentameric proton channel QQLL
E: De novo designed pentameric proton channel QQLL
F: De novo designed pentameric proton channel QQLL
G: De novo designed pentameric proton channel QQLL
H: De novo designed pentameric proton channel QQLL
I: De novo designed pentameric proton channel QQLL
J: De novo designed pentameric proton channel QQLL
K: De novo designed pentameric proton channel QQLL
L: De novo designed pentameric proton channel QQLL
M: De novo designed pentameric proton channel QQLL
N: De novo designed pentameric proton channel QQLL
O: De novo designed pentameric proton channel QQLL
P: De novo designed pentameric proton channel QQLL
Q: De novo designed pentameric proton channel QQLL
R: De novo designed pentameric proton channel QQLL
S: De novo designed pentameric proton channel QQLL
T: De novo designed pentameric proton channel QQLL


Theoretical massNumber of molelcules
Total (without water)61,21620
Polymers61,21620
Non-polymers00
Water1086
1
A: De novo designed pentameric proton channel QQLL
B: De novo designed pentameric proton channel QQLL
C: De novo designed pentameric proton channel QQLL
D: De novo designed pentameric proton channel QQLL
E: De novo designed pentameric proton channel QQLL


Theoretical massNumber of molelcules
Total (without water)15,3045
Polymers15,3045
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-77 kcal/mol
Surface area7600 Å2
MethodPISA
2
F: De novo designed pentameric proton channel QQLL
G: De novo designed pentameric proton channel QQLL
H: De novo designed pentameric proton channel QQLL
I: De novo designed pentameric proton channel QQLL
J: De novo designed pentameric proton channel QQLL


Theoretical massNumber of molelcules
Total (without water)15,3045
Polymers15,3045
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-76 kcal/mol
Surface area7250 Å2
MethodPISA
3
K: De novo designed pentameric proton channel QQLL
L: De novo designed pentameric proton channel QQLL
M: De novo designed pentameric proton channel QQLL
N: De novo designed pentameric proton channel QQLL
T: De novo designed pentameric proton channel QQLL


Theoretical massNumber of molelcules
Total (without water)15,3045
Polymers15,3045
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-74 kcal/mol
Surface area7020 Å2
MethodPISA
4
O: De novo designed pentameric proton channel QQLL
P: De novo designed pentameric proton channel QQLL
Q: De novo designed pentameric proton channel QQLL
R: De novo designed pentameric proton channel QQLL
S: De novo designed pentameric proton channel QQLL


Theoretical massNumber of molelcules
Total (without water)15,3045
Polymers15,3045
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-74 kcal/mol
Surface area7330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.246, 100.175, 50.498
Angle α, β, γ (deg.)90.000, 110.506, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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


Mass: 3060.802 Da / Num. of mol.: 20 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 1.87 Å3/Da / Density % sol: 34.12 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / Details: 0.22 M sodium citrate, 0.1 M Tris, pH 8.0

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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: Dec 22, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115832 Å / Relative weight: 1
ReflectionResolution: 3→42.76 Å / Num. obs: 8920 / % possible obs: 98.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 60.13 Å2 / CC1/2: 0.998 / Net I/σ(I): 6.6
Reflection shellResolution: 3→3.18 Å / Num. unique obs: 1419 / CC1/2: 0.815

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6MCT

6mct


Resolution: 3→27.28 Å / SU ML: 0.4446 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.3081
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2864 834 9.98 %
Rwork0.2511 7521 -
obs0.2549 8355 92.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.94 Å2
Refinement stepCycle: LAST / Resolution: 3→27.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4093 0 0 6 4099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00374172
X-RAY DIFFRACTIONf_angle_d0.5835689
X-RAY DIFFRACTIONf_chiral_restr0.0432777
X-RAY DIFFRACTIONf_plane_restr0.0023621
X-RAY DIFFRACTIONf_dihedral_angle_d14.68381354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.190.32821050.3078906X-RAY DIFFRACTION67.94
3.19-3.440.35551300.31181241X-RAY DIFFRACTION91.71
3.44-3.780.35231550.32441335X-RAY DIFFRACTION99.33
3.78-4.320.27471540.23981358X-RAY DIFFRACTION99.93
4.33-5.440.29881470.21941342X-RAY DIFFRACTION98.87
5.44-27.280.21621430.21091339X-RAY DIFFRACTION96.86
Refinement TLS params.Method: refined / Origin x: 10.0150986321 Å / Origin y: -28.9974188109 Å / Origin z: 16.1292433391 Å
111213212223313233
T0.488329354293 Å2-0.000101613827638 Å2-0.00505011376561 Å2-0.398486489734 Å2-0.0237394434991 Å2--0.458206474199 Å2
L0.695470445706 °2-0.0113532372645 °20.902005497609 °2-1.11162548866 °20.0271437188026 °2--1.62908603444 °2
S0.000363508927016 Å °-0.0491726759317 Å °-0.0875031912374 Å °-0.182454054961 Å °0.049954442719 Å °0.00796342650447 Å °0.118463363795 Å °-0.11232120555 Å °-0.0297675275334 Å °
Refinement TLS groupSelection details: all

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