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Basic information

Entry
Database: PDB / ID: 7udy
TitleDesigned pentameric channel QLLL
ComponentsDesigned channel QLLL
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: Designed channel QLLL
B: Designed channel QLLL
C: Designed channel QLLL
D: Designed channel QLLL
E: Designed channel QLLL
F: Designed channel QLLL
G: Designed channel QLLL
H: Designed channel QLLL
I: Designed channel QLLL
J: Designed channel QLLL
K: Designed channel QLLL
L: Designed channel QLLL
M: Designed channel QLLL
N: Designed channel QLLL
O: Designed channel QLLL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,60718
Polymers45,68715
Non-polymers9193
Water00
1
A: Designed channel QLLL
B: Designed channel QLLL
C: Designed channel QLLL
D: Designed channel QLLL
E: Designed channel QLLL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8427
Polymers15,2295
Non-polymers6132
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-82 kcal/mol
Surface area7910 Å2
MethodPISA
2
F: Designed channel QLLL
G: Designed channel QLLL
H: Designed channel QLLL
I: Designed channel QLLL
J: Designed channel QLLL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5366
Polymers15,2295
Non-polymers3061
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-83 kcal/mol
Surface area7190 Å2
MethodPISA
3
K: Designed channel QLLL
L: Designed channel QLLL
M: Designed channel QLLL
N: Designed channel QLLL
O: Designed channel QLLL


Theoretical massNumber of molelcules
Total (without water)15,2295
Polymers15,2295
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-84 kcal/mol
Surface area7370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.385, 84.837, 149.557
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
Designed channel QLLL


Mass: 3045.830 Da / Num. of mol.: 15 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
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: 1.96 Å3/Da / Density % sol: 37.16 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase
Details: 0.22 M sodium citrate, 0.1 M Tris, pH 8.0, 35% 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→74.78 Å / Num. obs: 14395 / % possible obs: 99.5 % / Redundancy: 8.5 % / Biso Wilson estimate: 46.53 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.155 / Net I/σ(I): 8.1
Reflection shellResolution: 2.4→2.53 Å / Rmerge(I) obs: 1.249 / Num. unique obs: 2034 / CC1/2: 0.831

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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→39.77 Å / SU ML: 0.3235 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.4173
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2507 688 4.81 %
Rwork0.2297 13619 -
obs0.2307 14307 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.45 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3044 0 63 0 3107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00133228
X-RAY DIFFRACTIONf_angle_d0.32414400
X-RAY DIFFRACTIONf_chiral_restr0.0295610
X-RAY DIFFRACTIONf_plane_restr0.0015461
X-RAY DIFFRACTIONf_dihedral_angle_d10.23711073
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.590.34711460.28922640X-RAY DIFFRACTION98.62
2.59-2.850.321420.26292702X-RAY DIFFRACTION99.61
2.85-3.260.26691360.25072709X-RAY DIFFRACTION99.75
3.26-4.10.25031350.22472727X-RAY DIFFRACTION99.65
4.1-39.770.21331290.2092841X-RAY DIFFRACTION98.84
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)
13.56572847376-1.10634855359-1.612980040626.654655444783.392234896552.584705168-0.3561295334280.351365514338-0.0509573640268-0.1316433928010.676897345847-0.596315563186-0.04303600390360.373632973807-0.3613267462880.631943142621-0.0551878471172-0.0250271270930.596394293108-0.006301820846590.777489726823-5.0438209567523.4322332527-19.9282165256
27.199960659430.164088538661.230227934850.533533097199-1.301057523823.56292262070.6023748654250.552765393029-0.485221447309-1.13936526428-0.33725667381-2.780813819890.08273952964310.416114716667-1.441090662090.4849732803930.0007387941330870.07816227490880.641262806859-0.04602511039990.686826938186-6.7758098660123.613372056-29.8025470743
38.917563124581.962962949191.777790229758.586513194741.852402640074.71482513496-0.6159763212020.8401046743410.553833831372-1.147089595781.192391381670.756813097355-0.3214316174690.179056616834-0.2993079532140.59186675273-0.0286858870167-0.0009654985544510.4778258949020.02281369305650.667150828154-16.192774268125.0393491084-31.0607150331
40.421702097627-0.1050493016620.3079731510970.7769280183760.5318836484730.700965583090.02704488240640.09052212844310.851342179155-1.051143305590.01163986562160.0922131549513-0.09034742851290.113662156913-0.2085307828970.400364711843-0.04317137405470.0897160802154-0.3808554199310.1056608117471.03497365072-20.81459860824.0762941117-21.8351566219
58.240223996720.1012176508511.298068091258.72053849558-2.189854734259.170694536740.267245448527-0.0241636525540.4495514918280.9214175502010.0302506513562-0.185300569855-0.6236521208950.0131598113091-0.5076939877860.569340001191-0.0007497022713550.02997723019440.5108223280040.03255640666560.621936138442-13.966322540724.7762125115-15.1193969622
60.2354141521810.3756512124860.8937692545962.356946280130.8495151739054.657410127780.273691050155-0.0222558970459-0.0149916150945-0.00600322330566-0.188616103387-0.9630074827460.7493914132030.836905462425-3.399497895670.32380333127-0.04741281979480.06108045522870.265690698813-0.1222585560010.7937457404339.3553045878122.0173970087-1.34818744373
77.469483454730.863810168209-0.7368592082082.883430077480.9909921668227.66122395439-0.4009023172120.5399902323210.626065468272-1.59130109841.17725982749-0.1378793523-0.6371545619420.464574214454-0.6005293181020.562201535896-0.02498272982230.02460817155590.498192875557-0.01960377085310.7720799128423.0552985082824.363636604-7.86223597592
80.804313893331-0.40777407053-1.094558124260.1865556805480.5356275296611.586755925220.04671993113390.4854232130590.780548514022-0.0844789926094-0.8277496239760.436312432855-0.973334076679-0.512433618959-2.054712996310.6468188499260.0495652015065-0.1942028940.3749665822220.01408478701550.904034299939-6.4332482348422.708268147-3.60985826751
91.563980997162.31171367870.1481869368883.77278207832-0.9456060069774.17353878205-0.09614670874370.3165419221580.5946740152860.989834707994-0.04652201568720.828688723821-0.277473379618-0.712120378527-0.221244665920.5135538869690.0143151274630.05204392584510.406007460882-0.01484798336750.865035023746-5.5694507864122.55491900355.68499813
100.153849561723-0.1829869335020.2099233031120.232326388192-0.2137635283260.2075703057410.2121784344130.06474907337390.499319484275-0.1373181378370.249864036356-0.420088074622-0.08000424809610.2564140636710.661575829340.342875308752-0.00743711214390.02558965398410.111889874613-0.2129190517760.776434630514.3455197194122.25792283517.95249286923
114.807633579561.918037325020.24548504642.00355892717-0.3873958576895.61872967152-0.1794303367330.143255657208-1.2008494233-2.076288024980.268615171057-0.5201277987180.846859027505-0.466955715912-0.01946503499510.515495215406-0.00837677175407-0.0522599477070.450815908740.0536009122770.6336625251813.034672751721.4159923072-31.862960623
126.74721338753-1.76507389253-1.611898769578.595135252171.374939647724.08784754748-0.0762269895957-0.452371212529-0.415822950751-0.0401924285141-0.249611792363-0.4135573772950.0866424916787-0.21313536734-0.07104671483050.5094853748130.0149300798690.04193173065240.4552517477960.08540162996470.62065094166222.529969421.4316813896-28.6912074075
136.4558627634-0.667531286477-1.125642774329.790674981622.155410611833.69166088697-0.0918205198478-0.487490685390.06067828953160.461058294222-0.01939831515340.510802097006-0.30698608334-0.06541163199250.02435394901250.3830930365140.0340387693135-0.05255535731420.3333185572650.0899351828170.5880419998122.031208397921.4740201658-18.5789912875
141.23538770658-2.529253584571.516325782049.17615946043-3.067828609421.90010697782-0.321192886930.495006408690.2749955825212.033458458770.3676633090870.991523683083-0.784376129014-0.09523963005180.2986451936970.393474762250.06912820898430.1204564856470.3978199601010.2078723562260.68770573771212.072939777521.6944412634-15.9596729847
150.4755129024430.7905301406140.9447224478081.577488030611.994701399922.65130171467-0.2913213694590.277315089073-0.9025172299080.7641534842210.3705685252381.675119139290.540173928056-0.157635641584-0.6307759660820.398264249390.01509481818840.09034018188520.3578814853080.1879737855981.003479440287.0287303522521.1695689191-24.0914519134
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA2 - 251 - 24
22chain BBB1 - 261 - 26
33chain CCC1 - 251 - 25
44chain DDD1 - 261 - 26
55chain EEE1 - 251 - 25
66chain FFF1 - 251 - 25
77chain GGG1 - 251 - 25
88chain HHH1 - 251 - 25
99chain III1 - 251 - 25
1010chain JJJ1 - 251 - 25
1111chain KKK1 - 251 - 25
1212chain LLL1 - 261 - 26
1313chain MMM1 - 261 - 26
1414chain NNN1 - 261 - 26
1515chain OOO1 - 251 - 25

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