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- PDB-8dp6: Crystal structure of Helicobacter pylori EgtU -

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Basic information

Entry
Database: PDB / ID: 8dp6
TitleCrystal structure of Helicobacter pylori EgtU
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
Osmoprotection protein
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 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 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3154
Polymers63,1222
Non-polymers1922
Water16,177898
1
A: Osmoprotection protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6572
Polymers31,5611
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Osmoprotection protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6572
Polymers31,5611
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.463, 58.395, 61.886
Angle α, β, γ (deg.)90.000, 109.537, 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
Components on special symmetry positions
IDModelComponents
11B-902-

HOH

21B-1031-

HOH

31B-1103-

HOH

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Components

#1: Protein Osmoprotection protein


Mass: 31561.236 Da / Num. of mol.: 2 / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 898 / 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: 2.27 Å3/Da / Density % sol: 45.87 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.3 M ammonium sulfate, 22% PEG4000, 0.2 M sodium acetate, pH 4.8

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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: 1.3→39.53 Å / Num. obs: 137306 / % possible obs: 99.1 % / Redundancy: 4.5 % / Biso Wilson estimate: 12.57 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.069 / Net I/σ(I): 8.4
Reflection shellResolution: 1.3→1.32 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 13237 / CC1/2: 0.324 / Rpim(I) all: 0.952 / % possible all: 84.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.3→39.53 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1803 1999 1.45 %
Rwork0.1704 135530 -
obs-135530 99.1 %
Solvent computationSolvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→39.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4369 0 10 898 5277
LS refinement shellResolution: 1.3→1.32 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)
11.226952665010.105634553603-0.2548412952551.17067905448-0.5990817672562.06591607746-0.02690173284210.0893990055196-0.0721052631155-0.128552251773-0.01424221423390.01260481785430.174395603554-0.02381243647390.03370144951550.0615214586879-0.00520467686716-0.003457588029580.059904852218-0.008101283397110.0742023145397-63.1977345251-12.1210334225-15.5612151832
20.6340334107540.117860502031-0.1368639656151.056878242410.254215296090.6720170975110.0118193681252-0.011563586367-0.0863153567289-0.04178563489470.00249088086523-0.06004439122060.1642466014350.0474271170729-0.02441998493750.06381934109880.0120312250864-0.008819180228970.05679095262280.0007970117859010.0787606422848-55.2297956286-15.0412869481-9.77063330266
31.14841694213-0.2958677474460.5353635477680.511964991544-0.08856738871511.019119741810.02221558183630.004645292103680.02126262681750.008842214667740.00755209469544-0.0365780740927-0.01161458004470.0653266056913-0.03860540532050.0370182128875-0.00237005825657-0.009567948181820.0560435074937-0.001989858390410.0586011558188-50.0634142952-5.15165445368-1.8712954603
40.8517615902490.545697193532-0.3074398230841.178616778730.1856700409451.648078819490.035847594215-0.04610360239510.03178746523290.102964041939-0.0304011210594-0.00551770935283-0.1168931964160.0399998581856-0.008997636813160.06234945313990.00235810943723-0.004694801822380.05405926861670.003143757569240.0508553458985-73.0301091494-2.6848021151318.0733990662
52.75520180388-0.770044697179-1.514123169863.752774980110.5405262986012.75520369997-0.117399267176-0.243183131766-0.4387271790760.573670933971-0.0196104966848-0.4393933260930.3307380978290.589497955897-0.03709169603670.1367585535030.00791803967738-0.05247539383450.2469645548840.02064652328680.186742344959-60.519568522-9.8723794834219.8509851894
60.68190361149-0.418135880588-0.6134835833771.667209447980.08604898637321.958226363430.0386778045893-0.0102191562332-0.06422217004170.0173699528771-0.05576183943450.06202168375220.09289587858250.1252483508250.00251063689690.0681583636720.0133287561627-0.005572637037640.07233913400820.01505614561280.058708723499-74.6138572685-11.804477294517.7839266991
71.392601912360.260131758701-0.6138343358920.476929814297-0.4194500485152.23856815431-0.00428660549319-0.0196907272387-0.0621227780611-0.03209426742790.004529211257240.02486396442730.08309245191450.07369602271470.04037700085910.04060897285880.00490169673335-0.01219625604570.05144266107740.004251753391170.0660341139192-75.2207666427-8.8578211556512.2199891091
80.685754201762-0.059721080848-0.670773915570.4803521613890.05134327047511.018729527980.0327912908355-0.01975734897980.01321156887850.0040442539902-0.002143970591440.0012907338583-0.07496121156680.0438339413274-0.03340965266750.0544892075663-0.00542720975235-0.01515409754590.05853636884660.002443600571380.0552628764685-68.4587547608-2.695185117288.29540538775
91.78704854526-0.604483311731-0.8760170123911.662257464250.1178582038941.835708576760.04189785521820.1274626236670.0623594823036-0.2522144526710.0157345774208-0.07351131721960.01545473855740.0851831469876-0.04970707466080.0771908479602-0.0213376928937-0.01110833324560.0748883090331-0.001529006176730.0577886465449-55.4356979483-3.32443628876-16.435678751
102.248737482480.7206995699430.3528448762090.7587126022550.2679657376381.52784659961-0.06754176574930.0233101910224-0.0547314008404-0.05877339518120.05915987841950.0451864876850.0113717749852-0.09459823944020.03476447777090.04103846443410.000258558764513-0.007530732887240.08004298809850.002890332852730.071861186036-76.0127169255-7.48911365438-5.00571464087
112.12086457220.77611401072-0.5069275873133.38932852099-0.9171641462141.842040949470.03967361411370.1972541405520.12875567955-0.0517300400818-0.04140712750440.0165075177116-0.152452167589-0.115022217236-0.009343182196630.07588012305880.000551521602135-0.01204455086240.1024986555090.01540369514650.100982967235-73.0679102447-4.48078328537-16.1624539554
121.108126459950.231127238564-0.002586404333411.58363072979-0.08144016659371.147070944390.0235787488471-0.03943878694270.08405086799110.0495659786007-0.001285802239220.0656644595255-0.141821589687-0.0477812633543-0.0287863256590.09623589213940.02017698909970.005755928518090.0791972918181-0.006248375529390.0876532907468-39.166161601-2.0287255423241.8020041258
131.496697941740.22994934381-0.2336042218511.500405005710.226257546891.12422298711-0.0124293494359-0.112852454472-0.0352143360266-0.02074773850970.0154168277211-0.2040976223540.02154512704210.1996760648150.000471443831710.0687953169725-0.003269920873610.0007893879299810.1105913098620.003240196482230.0947174301372-22.423931632-9.5522790126638.0595770446
140.307865562595-0.10499580163-0.1974415294960.3632668059940.107536776971.05787422948-0.0212461738629-0.00374612413056-0.0105540721544-0.00268825139257-0.01058526078380.002795207448680.03966672350460.02791981282120.03992953709370.0379215194506-0.00252336329976-0.007435446757860.041281638263-0.003401372021030.0742897018796-29.7005546691-13.610303539415.6050322128
150.534299911494-0.332696827677-0.2653637891012.602827712280.3502872996891.22684827195-0.0174632227711-0.09643073477220.188085620311-0.02015616536980.038562347756-0.121648168607-0.1325972645640.171872214799-0.02383094014780.0796010520876-0.0123054877702-0.02855471808860.126688408296-0.01059774943730.182196144369-18.5513705758-6.6056299275814.79366507
160.8204465729340.279562202072-0.4683190202121.344429465940.2036932614311.643584381760.0216503773244-0.07242160935290.107715605732-0.0190343198938-0.0119004418887-0.000568021560513-0.03388796473420.07376590752820.005853100542920.062219819766-0.00917146187699-0.007721834601490.06231058318160.003489023807560.0702738974143-30.6767686223-4.712728633957.73479931529
171.49024811963-0.360304476154-0.1502348158130.746405101193-0.551788276142.22826870445-0.0213294182159-0.01642639915720.0499463486259-0.001523960188610.00485347295777-0.00882213639458-0.0223826885907-0.01046660219350.03963917917790.054287451715-0.00882936263523-0.00629814355380.0447847100766-0.006144159000220.0705523797802-34.524108291-7.8481987796911.6254605592
183.6307360633-1.328941201970.1144489472650.787444953521-0.0187821452241.13871770545-0.0717732292859-0.007334486838-0.1176141538750.009151515785620.03908607318760.061499809740.0319107502392-0.08673803524540.04726649475950.0579794905984-0.006994024876380.001326957471230.06502783444480.0004768383450370.0831984728632-34.788480191-15.025904779415.7611738918
191.02120573007-0.199529095189-1.181738747620.9839805039220.1339442844243.08974468528-0.0593366832833-0.146866842511-0.04760248093170.177717086930.02905906693240.03777147455060.1025499347540.1774885755350.04535961389820.07840409074950.00466276445255-0.003546454959080.07830460140680.002847960006980.0709954765079-30.0031388059-10.023030006940.438150297
200.7798770169760.2294099306450.4389979713331.289112838371.330484106322.216474145650.114425692544-0.1295461774530.01367493458770.2292153173860.08566038803490.1685588703030.170476344123-0.146365024704-0.03022384587340.1270318406630.010600267660.03646420090470.1046437037730.01743522198250.105869186121-40.1009585467-16.50745891943.9810816314
212.440131106460.3232793156730.3586788004131.09261779932-0.5402456696371.52201235407-0.04485844536880.09121959496610.0136542279603-0.2336700296350.02867121097940.180252719396-0.293106736453-0.477948112453-0.01242688358370.1255890628690.0382934747464-0.03516273591530.17150303317-0.01582400376770.0732880212637-45.9400968435-9.3789766930724.3152778135
221.793492905010.196868146912-0.1235893503824.80810432941-1.5124921374.45815184355-0.01005968864510.113052796148-0.162362418905-0.0378203189244-0.008730094055030.5056852712120.135440828636-0.9292805407560.05696258156410.111086767782-0.03070063513860.007388349016020.218269324088-0.02253059488510.164211243361-50.7326034108-12.339002066234.8217721887
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 287 through 314 )AA287 - 3141 - 28
22chain 'A' and (resid 315 through 353 )AA315 - 35329 - 67
33chain 'A' and (resid 354 through 389 )AA354 - 38968 - 103
44chain 'A' and (resid 390 through 426 )AA390 - 426104 - 140
55chain 'A' and (resid 427 through 439 )AA427 - 439141 - 153
66chain 'A' and (resid 440 through 459 )AA440 - 459154 - 173
77chain 'A' and (resid 460 through 472 )AA460 - 472174 - 186
88chain 'A' and (resid 473 through 494 )AA473 - 494187 - 208
99chain 'A' and (resid 495 through 522 )AA495 - 522209 - 236
1010chain 'A' and (resid 523 through 539 )AA523 - 539237 - 253
1111chain 'A' and (resid 540 through 553 )AA540 - 553254 - 267
1212chain 'B' and (resid 288 through 341 )BC288 - 3411 - 54
1313chain 'B' and (resid 342 through 376 )BC342 - 37655 - 89
1414chain 'B' and (resid 377 through 426 )BC377 - 42690 - 139
1515chain 'B' and (resid 427 through 439 )BC427 - 439140 - 152
1616chain 'B' and (resid 440 through 459 )BC440 - 459153 - 172
1717chain 'B' and (resid 460 through 472 )BC460 - 472173 - 185
1818chain 'B' and (resid 473 through 488 )BC473 - 488186 - 201
1919chain 'B' and (resid 489 through 506 )BC489 - 506202 - 219
2020chain 'B' and (resid 507 through 522 )BC507 - 522220 - 235
2121chain 'B' and (resid 523 through 539 )BC523 - 539236 - 252
2222chain 'B' and (resid 540 through 553 )BC540 - 553253 - 266

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