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- PDB-8dp7: Structure of Helicobacter pylori EgtU bound to EGT -

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Basic information

Entry
Database: PDB / ID: 8dp7
TitleStructure of Helicobacter pylori EgtU bound to EGT
ComponentsOsmoprotection protein
KeywordsTRANSPORT PROTEIN / EgtU / EGT / transporter / ABC transporter
Function / homology
Function and homology information


glycine betaine transport / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex
Similarity search - Function
: / ABC-type glycine betaine transport system, substrate-binding domain / Substrate binding domain of ABC-type glycine betaine transport system / ABC transporter type 1, transmembrane domain MetI-like / MetI-like superfamily / Binding-protein-dependent transport system inner membrane component / ABC transporter integral membrane type-1 domain profile.
Similarity search - Domain/homology
Chem-LW8 / Osmoprotection protein
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsDuncan-Lowey, B. / Zhou, W. / Kranzusch, P.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell / Year: 2022
Title: A microbial transporter of the dietary antioxidant ergothioneine.
Authors: Dumitrescu, D.G. / Gordon, E.M. / Kovalyova, Y. / Seminara, A.B. / Duncan-Lowey, B. / Forster, E.R. / Zhou, W. / Booth, C.J. / Shen, A. / Kranzusch, P.J. / Hatzios, S.K.
History
DepositionJul 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 1.2Dec 7, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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: Osmoprotection protein
B: Osmoprotection protein
C: Osmoprotection protein
D: Osmoprotection protein
E: Osmoprotection protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,95810
Polymers157,8065
Non-polymers1,1525
Water00
1
A: Osmoprotection protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7922
Polymers31,5611
Non-polymers2301
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Osmoprotection protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7922
Polymers31,5611
Non-polymers2301
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Osmoprotection protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7922
Polymers31,5611
Non-polymers2301
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Osmoprotection protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7922
Polymers31,5611
Non-polymers2301
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Osmoprotection protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7922
Polymers31,5611
Non-polymers2301
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)134.716, 137.751, 190.496
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#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
Osmoprotection protein


Mass: 31561.236 Da / Num. of mol.: 5 / Fragment: UNP residues 245-516
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain P12) (bacteria)
Strain: P12 / Gene: proWX, HPP12_0825 / Production host: Escherichia coli (E. coli) / References: UniProt: B6JM49
#2: Chemical
ChemComp-LW8 / trimethyl-[(2S)-1-oxidanyl-1-oxidanylidene-3-(2-sulfanylidene-1,3-dihydroimidazol-4-yl)propan-2-yl]azanium


Mass: 230.307 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H16N3O2S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.8 Å3/Da / Density % sol: 56.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 0.1 M sodium acetate, 22% PEG4000

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.35→39.54 Å / Num. obs: 25843 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 102.64 Å2 / CC1/2: 0.854 / Rpim(I) all: 0.42 / Net I/σ(I): 4.3
Reflection shellResolution: 3.35→39.54 Å / Mean I/σ(I) obs: 1 / Num. unique obs: 4620 / CC1/2: 0.119 / Rpim(I) all: 3.422 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 8DP6

8dp6


Resolution: 3.35→39.54 Å / Cross valid method: FREE R-VALUE / σ(F): 1.33
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.288 1978 -
Rwork0.231 22347 -
obs-24325 94.09 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 97.65 Å2
Refinement stepCycle: LAST / Resolution: 3.35→39.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10855 0 75 0 10930
LS refinement shellResolution: 3.35→3.58 Å
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)
14.14289381646-0.210171162011-0.1834621909393.43002235086-2.385783938343.90951641166-0.300656592775-0.43423668717-0.08738028829560.6741754698640.1315996616560.0934904854524-1.155930207030.332564836730.1914040753681.686122877290.16823389405-0.1700501199820.6819220490830.1197071816350.62904205677230.188986015449.0666988651-9.2179298451
21.648418867740.8399351680012.33847319742.020001820040.7141909848336.49547221806-0.14662925122-0.759146613763-0.9116336110920.5182357707010.2996816215150.6370131006970.0812237408362-0.859603245368-0.215743362481.422152013470.4101865243010.3567761918241.092271770270.6085170734010.79924529090126.331479278124.85614634882.78713597629
34.009548238260.170774646691-0.9622349802963.02128262215-0.1666815509323.4913743819-0.660518614504-0.8707153715020.1569942422960.1685503292820.5138656338420.406175999647-1.44931689988-0.2367342859-0.02532009670631.459172164960.265264379747-0.06104868681070.8635985822320.1445094985160.61876191151423.578173702342.8507213635-2.11983679173
45.872241499872.73259295567-1.197003006724.63628571205-0.7800596190381.086882498610.933503001034-0.1056458775780.383865212777-0.536025801124-0.8925846003791.37372629471-0.559113593792-0.692761654747-0.3707755934911.752794359890.7551208475920.1226149769181.33247753260.05023492887771.0259695498811.728145641150.8873019212-2.03566849109
52.45413941727-0.681215074066-0.3279987427292.08267704774-1.190612014092.61434340025-0.0649739687236-0.1946723546590.641984023394-0.281309321141-0.02359223951560.2557003058420.431367438782-0.1281325609750.1420195174031.11843052651-0.126179801972-0.2110277988360.651273563842-0.3049691516330.89738287649334.987312379352.072443732175.3936765823
61.375472793230.8838253457361.166759300433.6836509790.4554672542611.33053013679-0.1614103134620.4441681379481.58185935164-0.3364514789830.246367151267-0.573254284091-0.8701187229860.0317456988767-0.5391743841.60155296661-0.0639539484875-0.1894869961340.622543339888-0.2571186223741.5399261464638.916944926163.243481873269.9058075356
74.38204690171-1.50435830388-2.582840153415.811617220231.826917858794.796044764060.7709666181760.20584245847-0.25899055005-0.691858538261-0.182690215936-0.3758726876950.421357775198-0.5715905271530.03013851468230.94937222395-0.299806917503-0.4258571602270.5918033711320.07409455545330.978291776008-0.49396354884246.095007956949.8774603219
83.29991789062-2.7933140959-2.732897431534.983297754261.036297958287.213311036090.13063343045-0.930038389008-0.5947129081331.56264237210.398354836091-0.398238454160.1496051111880.244932056083-0.3781146259590.822493539726-0.140160435438-0.2031500729450.7854588849330.182371141640.9872713442466.3845022021448.737553123565.4087996768
91.232847299550.7205988322361.13135505434.07776647205-1.874706533344.724561466460.245355368035-0.01949812251130.836639059737-0.6534360337270.189516569573-0.4646181116980.1256556665560.102024685158-0.06182559820220.548584100619-0.4312006488890.04950757050710.766049757485-0.3224903880011.2570209274615.54388440869.596466581454.0252607181
103.31645123413-2.15134663683-1.312666076211.396382939210.9830673942453.3130184228-0.15414218212-0.783481511972-1.1918951649-0.7432317632220.0762328039006-0.524047265280.4431410609530.0465000399236-0.1206682198290.579451954581-0.123047301343-0.2055675763050.5564989810840.1440721284590.9635415284557.7122858750943.568647577358.6422301773
113.49451337065-1.59406219187-0.4435784041632.63722003221-0.441569888792.81550009240.5712239112740.4504140978670.2125540883-0.0614329447199-0.0159817497668-0.37196246638-1.199779897710.876006362121-0.3285890692290.589650224411-0.179873242242-0.09854289740740.7399435853870.1082379523811.3581892357717.113675959550.510323982642.6950958997
123.791326218463.403190765071.682715043925.43890029103-1.332054863544.14032613643-0.753448841595-0.0553773810096-0.732277343732-2.08564613799-0.290194018727-0.633165617748-1.71692367019-0.4817796053531.079548426751.23961106920.2091960907840.2832964413320.692799663397-0.1205437549990.74747036303812.203701376739.705199559941.3980296439
131.81813344823-1.113478313842.376956750162.99929482948-0.5679669337614.358141060680.08155459886950.07675044922911.614896453430.1697999821420.084435549653-0.102347119361-0.008923985698750.307930926463-0.3068021083860.6143856538890.03239278825040.05323155465610.483676418059-0.1763391082511.3788378333147.267738157876.646087684531.4595578946
143.799783068823.2262391655-0.3692070607512.73877060826-0.1968703211876.68549691654-0.0199082644288-0.470755894082-0.02632089119110.625433615220.303291858231-0.2745532196851.078921217420.158370873804-0.145919805520.501980163740.368958096482-0.2450327687430.777387077713-0.2875871913620.76616087563556.733497864155.764405621841.0784593741
151.74234986262-0.579126054989-0.9444866093972.94533313249-0.7014148360253.49084702904-0.0600454142436-0.7427023168021.753058754310.225112221456-0.1311357831340.779372291041-0.5056472746210.3014360892640.1926636497980.714725557097-0.198789582099-0.05953939884470.653108239973-0.2835911646631.9303377061147.90208663682.829959741242.3123522301
167.808417607391.03063304878-1.231605895354.51491956405-0.06468382214382.994083032-0.0157591161770.382264859710.02680867969490.1414584084370.244255194829-0.08838964295650.6404338595320.182345570754-0.04851390871781.070155608950.184240297857-0.1380989139390.53065916530.03405788496960.43543006979243.766649986533.722988131528.4385133137
177.06057906407-0.0289361258489-2.100603215294.476473105252.163628842597.571510052290.1694375346160.01663656118280.591669952424-0.8198012078390.003795784562430.856307641196-0.385320644465-0.491713504937-0.1394611857640.871216583829-0.000429633352835-0.315021417570.4619962484660.1812021118880.86782043542832.560385125657.004185887522.8706113206
182.196135544881.78011994540.6654881724522.64860171735-0.9177402472593.33323990457-0.1804894887470.6108537980040.508259401707-0.402202181154-0.02150965781741.171477102770.332649843809-0.173011545870.2082763924680.7430549923630.023507251103-0.2436243367510.6144704053650.08472322643940.97854928883128.687966390549.321790857822.8815686699
192.892960103341.393810732070.8522990446883.48197028789-1.898244463632.151457218650.2512636569310.335039085505-1.39426873678-0.422514363036-0.457007588692-0.7248125067331.668318928780.0341112282117-0.4254839588211.820962772730.265780803599-0.120696611560.410887844258-0.2360832667250.87302379179442.869775135522.872828333928.859724671
207.924922728170.0522602046183-0.9397991523674.84508324685-0.7052024390296.397252039570.396038234551-0.5719290574881.326371539460.0351864809117-0.3187986106810.4151424859550.403735765976-0.487829473882-0.1598601918460.8500515388740.178611689452-0.1446639583810.7635352051630.08475819928070.71816484627323.470556746136.315237501432.2594884162
217.89085603207-5.42197325076-4.541241039739.283620544226.47551141764.636132079980.466023720633-0.479524349372-1.245219958240.535707537537-1.289117677332.364810019260.0701430386343-0.4834930911241.238191027191.84062193146-0.3271363116520.09541112521250.525977049149-0.1048387030931.0491593122926.574948848625.471525812235.7659251997
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 289 through 389 )AA289 - 3891 - 101
22chain 'A' and (resid 390 through 450 )AA390 - 450102 - 162
33chain 'A' and (resid 451 through 522 )AA451 - 522163 - 234
44chain 'A' and (resid 523 through 553 )AA523 - 553235 - 265
55chain 'B' and (resid 289 through 472 )BC289 - 4721 - 184
66chain 'B' and (resid 473 through 553 )BC473 - 553185 - 265
77chain 'C' and (resid 289 through 341 )CE289 - 3411 - 53
88chain 'C' and (resid 342 through 389 )CE342 - 38954 - 101
99chain 'C' and (resid 390 through 483 )CE390 - 483102 - 195
1010chain 'C' and (resid 484 through 522 )CE484 - 522196 - 234
1111chain 'C' and (resid 523 through 539 )CE523 - 539235 - 251
1212chain 'C' and (resid 540 through 553 )CE540 - 553252 - 265
1313chain 'D' and (resid 289 through 389 )DG289 - 3891 - 101
1414chain 'D' and (resid 390 through 494 )DG390 - 494102 - 206
1515chain 'D' and (resid 495 through 553 )DG495 - 553207 - 265
1616chain 'E' and (resid 289 through 389 )EI289 - 3891 - 101
1717chain 'E' and (resid 390 through 459 )EI390 - 459102 - 171
1818chain 'E' and (resid 460 through 494 )EI460 - 494172 - 206
1919chain 'E' and (resid 495 through 522 )EI495 - 522207 - 234
2020chain 'E' and (resid 523 through 539 )EI523 - 539235 - 251
2121chain 'E' and (resid 540 through 553 )EI540 - 553252 - 265

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