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- PDB-7udv: Designed pentameric proton channel LLQL -

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Basic information

Entry
Database: PDB / ID: 7udv
TitleDesigned pentameric proton channel LLQL
ComponentsDe novo designed proton channel LLQL
KeywordsMEMBRANE PROTEIN / Proton transport / de novo designed / pentameric
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 proton channel LLQL
B: De novo designed proton channel LLQL
C: De novo designed proton channel LLQL
D: De novo designed proton channel LLQL
E: De novo designed proton channel LLQL
F: De novo designed proton channel LLQL
G: De novo designed proton channel LLQL
H: De novo designed proton channel LLQL
I: De novo designed proton channel LLQL
J: De novo designed proton channel LLQL


Theoretical massNumber of molelcules
Total (without water)30,45810
Polymers30,45810
Non-polymers00
Water724
1
A: De novo designed proton channel LLQL
B: De novo designed proton channel LLQL
C: De novo designed proton channel LLQL
D: De novo designed proton channel LLQL
E: De novo designed proton channel LLQL


Theoretical massNumber of molelcules
Total (without water)15,2295
Polymers15,2295
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-80 kcal/mol
Surface area7240 Å2
MethodPISA
2
F: De novo designed proton channel LLQL
G: De novo designed proton channel LLQL
H: De novo designed proton channel LLQL
I: De novo designed proton channel LLQL
J: De novo designed proton channel LLQL


Theoretical massNumber of molelcules
Total (without water)15,2295
Polymers15,2295
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-82 kcal/mol
Surface area7290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.530, 55.360, 82.710
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

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Components

#1: Protein/peptide
De novo designed proton channel LLQL


Mass: 3045.830 Da / Num. of mol.: 10 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 1.97 Å3/Da / Density % sol: 37.7 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase
Details: 0.2 M magnesium chloride, 0.1 M potassium chloride, 0.03 M sodium citrate, pH 4, 33% 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-D / Wavelength: 1.03318 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03318 Å / Relative weight: 1
ReflectionResolution: 2.4→46.01 Å / Num. obs: 8089 / % possible obs: 91.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 40.44 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Net I/σ(I): 7.6
Reflection shellResolution: 2.4→2.465 Å / Rmerge(I) obs: 0.826 / Num. unique obs: 405 / CC1/2: 0.591

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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: 2.4→46.01 Å / SU ML: 0.2394 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.1145
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2676 428 5.32 %
Rwork0.2462 7620 -
obs0.2474 8048 81.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.89 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2035 0 0 4 2039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00272073
X-RAY DIFFRACTIONf_angle_d0.4982827
X-RAY DIFFRACTIONf_chiral_restr0.0345397
X-RAY DIFFRACTIONf_plane_restr0.0022299
X-RAY DIFFRACTIONf_dihedral_angle_d12.6408675
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.750.31761090.25461971X-RAY DIFFRACTION64.38
2.75-3.460.27821340.25782594X-RAY DIFFRACTION83.71
3.46-46.010.25571850.23993055X-RAY DIFFRACTION95.13
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)
14.91046636968-0.3689785166190.3845308961534.245797311-0.8791035051833.394028000160.07760873847360.260989806671-0.278435202274-0.508278820651-0.03000495255020.1060482994850.453656686571-0.7007449758080.1284362215420.260227034678-0.05271364764230.04172613732740.42266203272-0.02281870682350.210503923582-6.5576199105-1.5414153822-17.7991195784
23.33594086032-0.150598997896-0.490181392932.14940600886-0.5736903535161.236544557370.3702279011990.7215104038050.346745523435-0.3843119386750.183813151279-0.01744764772780.09555374760450.1497982412910.5802331902840.3674777220230.03581762992820.003657992862050.242732496407-0.003795420465840.1489245411563.58988147541-2.94112534938-18.6814918178
33.474746713420.610143751849-0.4946349137683.1360948471.842328306265.15070052331-0.168062519555-0.10679307238-0.0769636136291-0.1855120802870.00246509672333-0.1372144690670.03969964021210.1073540042920.134152977330.340974312955-0.02644801453960.01241999973030.36719237511-0.0113206940640.2993033822647.788513272335.65750565327-17.8126309215
45.322407679-1.452269970114.973326327313.69525133972-2.84995313045.313343735160.3550048370450.454535873716-0.289062346243-0.1931806244020.1570941901-0.4689013608980.1828224866910.7432388907832.649598633060.4435747611-0.07511479492050.02022194769620.208009694960.08523324455240.3419996985740.60465691315212.690548523-18.5187931188
54.11412195334-0.762585435927-1.028183325182.15114222296-0.7555906077043.250881960680.366856852537-0.121101187063-0.00988558709488-0.03013306158410.2104543015610.203712163503-0.182871469925-0.7433284445690.2480015664650.2621167481940.0794805791031-0.04510728954140.2955743991370.01292992919580.243881739439-8.294729311687.5344382617-19.6851365942
61.73043685781-0.2956310517251.120092686723.67386794851-0.7411192013442.980265136230.177618809260.2030344393720.490669889921-0.1033426425150.2511987969460.2873998621261.27219127990.05897387362630.1279455436090.4656742812720.0484701363069-0.05975497200210.5191851703450.04397657433780.2594524567-21.9870912538-11.5158576477-22.0121103367
73.0997624536-0.716160050240.1128470061671.55586798618-0.00274933489710.00473081663708-0.0291338324478-0.123633341020.5274043550680.2272355949670.30609321596-0.4656789941562.698360506130.1642771295281.337640113860.710355924142-0.0658613180624-0.05585316078550.5756779622420.03365754191450.337159294321-31.8018990398-11.1099082619-21.4789437831
82.03077963249-0.7148704391242.276588472231.93652074579-1.052698247326.510145489030.121668193122-0.712629866021-0.121896904051-0.06019174629470.1231575788490.325949897519-0.985022275527-1.018487715440.1980975222390.289711975853-0.0867959669157-0.002603524786130.3698799382490.01347220523440.307810959392-34.6461248464-2.13077429464-22.5264261296
92.16135635474-1.50469238506-1.044302229876.16365812288-0.4047278286625.19064166980.418586342739-0.0661756014686-0.189140151822-0.07225752404990.2060540736430.2448940299620.0484430705577-0.9982369131810.03092217771970.472744320497-0.0193773755779-0.03832527339120.4453533363350.01223818475170.378635064146-26.55875810713.65198844698-22.5202652585
102.577746979210.3746204495970.4966272181214.00123410973-1.015037762762.74720124610.06794087516050.096521295125-0.178204287750.01038762331160.000919819972588-0.426772790528-0.5462485966350.412578376268-0.2941887411830.278330362232-0.04696242226930.02321041492570.522678841868-0.1134349728890.1583013758-18.3481362628-2.26537982665-21.9718501834
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 24 )AA1 - 241 - 24
22chain 'B' and (resid 1 through 25 )BB1 - 251 - 25
33chain 'C' and (resid 1 through 25 )CC1 - 251 - 25
44chain 'D' and (resid 1 through 25 )DD1 - 251 - 25
55chain 'E' and (resid 2 through 26 )EE2 - 261 - 25
66chain 'F' and (resid 1 through 25 )FF1 - 251 - 25
77chain 'G' and (resid 2 through 26 )GG2 - 261 - 25
88chain 'H' and (resid 1 through 25 )HH1 - 251 - 25
99chain 'I' and (resid 1 through 25 )II1 - 251 - 25
1010chain 'J' and (resid 1 through 26 )JJ1 - 261 - 26

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