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- PDB-7udz: Designed pentameric proton channel LQLL -

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Basic information

Entry
Database: PDB / ID: 7udz
TitleDesigned pentameric proton channel LQLL
ComponentsDe novo designed pentameric proton channel LQLL
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: 2.48 Å
AuthorsKratochvil, H.T. / Thomaston, J.L. / Mravic, M. / Nicoludis, J.M. / 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 LQLL
B: De novo designed pentameric proton channel LQLL
C: De novo designed pentameric proton channel LQLL
D: De novo designed pentameric proton channel LQLL
E: De novo designed pentameric proton channel LQLL
F: De novo designed pentameric proton channel LQLL
G: De novo designed pentameric proton channel LQLL
H: De novo designed pentameric proton channel LQLL
I: De novo designed pentameric proton channel LQLL
J: De novo designed pentameric proton channel LQLL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,52813
Polymers30,45810
Non-polymers1,0703
Water724
1
A: De novo designed pentameric proton channel LQLL
B: De novo designed pentameric proton channel LQLL
C: De novo designed pentameric proton channel LQLL
D: De novo designed pentameric proton channel LQLL
E: De novo designed pentameric proton channel LQLL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5866
Polymers15,2295
Non-polymers3571
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-79 kcal/mol
Surface area7290 Å2
MethodPISA
2
F: De novo designed pentameric proton channel LQLL
G: De novo designed pentameric proton channel LQLL
H: De novo designed pentameric proton channel LQLL
I: De novo designed pentameric proton channel LQLL
J: De novo designed pentameric proton channel LQLL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9427
Polymers15,2295
Non-polymers7132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-79 kcal/mol
Surface area7320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.772, 46.658, 66.320
Angle α, β, γ (deg.)90.000, 108.955, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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


Mass: 3045.830 Da / Num. of mol.: 10 / 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.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.08 Å3/Da / Density % sol: 40.99 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase / Details: 0.1 M calcium chloride, 0.1 M MES, 29% v/v PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03318 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 2.47→41.03 Å / Num. obs: 8896 / % possible obs: 98.1 % / Redundancy: 3.2 % / Biso Wilson estimate: 43.68 Å2 / CC1/2: 0.991 / Net I/σ(I): 8.1
Reflection shellResolution: 2.47→2.61 Å / Rmerge(I) obs: 0.708 / Num. unique obs: 1248 / CC1/2: 0.8

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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: 2.48→36.87 Å / SU ML: 0.2399 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.9364
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2693 466 5.24 %
Rwork0.2477 8430 -
obs0.2488 8896 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.12 Å2
Refinement stepCycle: LAST / Resolution: 2.48→36.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2024 0 21 4 2049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022099
X-RAY DIFFRACTIONf_angle_d0.41412855
X-RAY DIFFRACTIONf_chiral_restr0.0305398
X-RAY DIFFRACTIONf_plane_restr0.0017298
X-RAY DIFFRACTIONf_dihedral_angle_d12.8777693
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.840.35171460.27932789X-RAY DIFFRACTION98.42
2.84-3.580.3211660.2572830X-RAY DIFFRACTION99.34
3.58-36.870.22371540.23442811X-RAY DIFFRACTION96.64
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)
16.91666691030.4262077326662.191751044922.391712749580.1782272774043.49497811631-0.362302972306-0.0602188343720.1808230444470.144746769386-0.0704619427307-0.278854523944-0.4729408673070.329387353150.01693347700820.2123651086180.0448708346956-0.1375199696240.4079255945520.02930763501470.48319086915115.4169069145-26.697150776727.0700697699
27.035602537960.1366289717591.365708763422.62977931746-0.4566085123583.22396454710.30448597093-0.447854173767-0.4242720861330.2644610952480.511861149827-0.3382435659730.03061464768450.205675805050.1548747658750.06421691407170.010540152262-0.06072605878020.319972758421-0.1361653405360.4153780686617.6884513596-22.145902629818.0482122268
35.45367259180.3810586774542.161834420712.965634058210.2523125818954.51654437023-0.562442448040.5924398831371.85558043022-0.3305154851390.6044741002870.431402703092-0.443669731949-0.3175084639940.1310411906680.36226910944-0.00777607619726-0.05442601059220.3526306109640.07900526919370.50028873605217.4969865279-12.575345450219.1344271738
40.270073471829-0.6812371277480.5658458456212.72822654974-1.581128131092.174619080260.766371885954-0.639681072160.182509409021-0.0152946498706-0.7979525011290.1098110634360.309443439958-0.223019412622-0.1322167724560.250371208997-0.0347350333127-0.0630157916120.466017943514-0.2297470384880.58737854935813.0493960961-10.81902304328.2733238891
52.399783466620.5496040579891.069029609924.62254626840.02568750885783.7381072006-0.1219818210590.7892213043020.5044856074480.03639087640490.2130182543660.108954633729-0.1000287027030.4777935995380.09907942099790.1862100555480.0518636008089-0.001865997571810.401032794309-0.02767365614940.32007757328212.2736033263-19.445603028232.7299337065
69.70231013874-0.4257379929332.92555287795.255458984820.4088484782195.357760292040.242761697406-0.6407845387920.04027469307810.261583972868-0.281064734797-0.02324424055280.471937121963-0.584423571252-0.1112814518590.2988184214810.03814817031010.06457396346690.2710620205350.05209947835540.50290006324816.8580020197-47.08795182753.92572586142
74.896849242210.1472803297311.517345344182.322165869170.3188622893976.507511724450.0899956896913-1.19579992276-0.6441867492640.490842912397-0.0189780269771-0.5860270479290.179736927523-0.0487590705510.05761274993210.3351959756860.0123205960156-0.07399508908580.3568926664360.1172424950110.40989219415315.2315577229-42.767889835813.4730352168
85.05144026002-1.58917217919-0.1673380853254.307044483822.234702171864.8348711970.0548242520508-0.3424020259820.291443177698-0.0307758395469-0.2962638791160.4249817238480.422425539384-0.3102836161440.09951962308090.2854437852240.0457149265286-0.01729246824530.295770620006-0.04735456335990.25837919996715.295284608-33.25422327812.2545717278
92.7868970110.777317729860.2003519799344.073320912461.346392409373.019064260610.3259853292390.1797544597140.260371552153-0.0620683411451-0.4549900062650.09859913857060.1935953744330.0100614520788-0.05424470264580.344847685642-0.0241229562442-0.04958847308410.3945911961139.83596763067E-50.49477091933819.4074456484-31.21572967733.17612846907
102.81573108926-0.2477677659551.626648754742.36474165851-0.5737484091673.37124618043-0.108161192255-0.275672337652-0.835582507440.2036720542780.2984438340310.2263760940870.02699233900160.01880817121570.1768140357850.384717844241-0.07431941959450.1268372506550.3357833148570.01654923532590.49253515486620.9522281049-39.9661563751-1.44567405485
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA1 - 241 - 24
22chain BBB1 - 251 - 25
33chain CCC1 - 251 - 25
44chain DDD2 - 251 - 24
55chain EEE1 - 251 - 25
66chain FFF1 - 241 - 24
77chain GGG1 - 251 - 25
88chain HHH1 - 251 - 25
99chain III2 - 251 - 24
1010chain JJJ1 - 251 - 25

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