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- PDB-9egh: Crystal Structure of EgtUC binding domain mutant I243A bound to L... -

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Basic information

Entry
Database: PDB / ID: 9egh
TitleCrystal Structure of EgtUC binding domain mutant I243A bound to L-Ergothioneine from S. pneumoniae
ComponentsErgothioneine transporter EgtUC
KeywordsTRANSPORT PROTEIN / L-ergothioneine / ABC transporter / S. pneumoniae
Function / homology
Function and homology information


ABC-type quaternary ammonium compound transporting activity / quaternary ammonium group transport / glycine betaine transport / amino acid transport / 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 / Ergothioneine transporter EgtUBC
Similarity search - Component
Biological speciesStreptococcus pneumoniae D39 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsLegg, K.A. / Gonzalez-Gutierrez, G. / Giedroc, D.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118157 United States
CitationJournal: To Be Published
Title: C-H...S hydrogen bonds are essential for molecular recognition of ergothioneine by the bacterial ergothioneine transporter EgtUC in Streptococcus pneumoniae.
Authors: Legg, K.A. / Gonzalez-Gutierrez, G. / Edmonds, K.A. / Shushkov, P.G. / Giedroc, D.P.
History
DepositionNov 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ergothioneine transporter EgtUC
B: Ergothioneine transporter EgtUC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5134
Polymers62,0532
Non-polymers4612
Water4,107228
1
A: Ergothioneine transporter EgtUC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2572
Polymers31,0261
Non-polymers2301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ergothioneine transporter EgtUC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2572
Polymers31,0261
Non-polymers2301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.161, 129.204, 206.464
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Space group name HallF22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x,y+1/2,z+1/2
#6: x,-y+1/2,-z+1/2
#7: -x,y+1/2,-z+1/2
#8: -x,-y+1/2,z+1/2
#9: x+1/2,y,z+1/2
#10: x+1/2,-y,-z+1/2
#11: -x+1/2,y,-z+1/2
#12: -x+1/2,-y,z+1/2
#13: x+1/2,y+1/2,z
#14: x+1/2,-y+1/2,-z
#15: -x+1/2,y+1/2,-z
#16: -x+1/2,-y+1/2,z
Components on special symmetry positions
IDModelComponents
11A-727-

HOH

21A-754-

HOH

31A-818-

HOH

41B-777-

HOH

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Components

#1: Protein Ergothioneine transporter EgtUC


Mass: 31026.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae D39 (bacteria)
Gene: proWX, SPD_1642 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2ZQB9
#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.: 2 / Source method: obtained synthetically / Formula: C9H16N3O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.17 Å3/Da / Density % sol: 61.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Sodium citrate tribasic pH 5.6, Potassium Sodium Tartrate 0.2 M and Ammonium Sulphate 1.6 - 2.0 M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.14→118.16 Å / Num. obs: 23521 / % possible obs: 88.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 31.16 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.051 / Rrim(I) all: 0.119 / Rsym value: 0.107 / Net I/σ(I): 8.3
Reflection shellResolution: 2.14→2.49 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1176 / CC1/2: 0.865 / Rpim(I) all: 0.213 / Rrim(I) all: 0.363 / Rsym value: 0.29

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→40.16 Å / SU ML: 0.2427 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.9343
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2682 1163 4.97 %
Rwork0.2263 22228 -
obs0.2285 23391 53.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.12 Å2
Refinement stepCycle: LAST / Resolution: 2.14→40.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4292 0 30 228 4550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00494398
X-RAY DIFFRACTIONf_angle_d0.85975944
X-RAY DIFFRACTIONf_chiral_restr0.0504662
X-RAY DIFFRACTIONf_plane_restr0.0066772
X-RAY DIFFRACTIONf_dihedral_angle_d7.0597590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.230.319460.3578113X-RAY DIFFRACTION2.23
2.23-2.350.195760.3247303X-RAY DIFFRACTION5.73
2.35-2.50.3394300.3132759X-RAY DIFFRACTION14.61
2.5-2.690.3833950.30371946X-RAY DIFFRACTION37.64
2.69-2.960.34172190.29513781X-RAY DIFFRACTION73.52
2.96-3.390.30852690.25925061X-RAY DIFFRACTION97.55
3.39-4.270.2792670.20515045X-RAY DIFFRACTION96.76
4.27-40.160.19822710.19055220X-RAY DIFFRACTION97.01
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)
12.47688383812-0.369586610176-0.476811978723.5598866304-0.3980651133593.04283251572-0.0516573426157-0.01919598108070.003793474471450.233046664102-0.0189165713176-0.2246399789310.1230556852280.2302685678520.01016770580330.3259739196790.0786011683689-0.02956951399880.2352281958920.02146664144860.2522738922746.1952344911955.853532631552.0287060204
22.7801195677-0.825874970951-0.9512977747451.78153204280.3891255988193.03608109999-0.04919886475040.148127926652-0.120128561623-0.017064658488-0.123119728138-0.218884086360.5292092853210.1199924442720.03607394499270.346763299650.139574985196-0.003142228526780.2673415404390.06006656044650.3298993058267.5490136999942.981677413540.0746208592
31.60435298724-0.3271204571431.23858768164.770270061790.5586176667844.32106457634-0.2034431957190.3648199847770.149001836964-0.127345298218-0.1040997162090.662455472294-0.0635722104591-0.6385455610550.2805706992450.3173041849870.0535831039162-0.04045764672320.403516837212-0.0515505009910.331828084219-10.796966556553.929516679328.3939671453
41.814014744950.3298863311520.9052184753432.23606139760.2814687544613.600986884210.157038011273-0.230900795431-0.1470290466890.316259663353-0.2227797458210.03230794168880.468766620629-0.3204693861670.04865524600420.3853090219770.0206894691650.03614273951510.2924096113630.02581571254460.240469473447-1.6595816541147.221281764351.2023787959
52.46485746051-0.4084830198250.1182226434423.42427149239-0.2729958240864.28051743055-0.06789536528050.7275813261160.298008111063-0.351777978842-0.173643327665-0.1149215621840.06237140619450.2374008616370.2450153845920.3026259593110.00240520967092-0.02949182987480.4479510322690.06682001553560.24531774015322.340043907241.32980133780.897954654233
61.910365354160.47773561981-0.6168643889913.018437852480.3849032492462.71706471784-0.11296616992-0.2750371180680.1658613925310.4654908131540.04780887663720.3442052613030.522618989070.1169187195020.01394093097060.3582535029020.167613588926-0.01831659451370.275844523532-0.02499740939350.31101867977710.46515780342.385610988116.7194589788
72.042710731710.890419075009-0.2724458503932.922379905140.1854927083882.50163396871-0.3289784026350.06542929612840.562696623671-0.429762928379-0.1332472810250.441162788964-0.452657388317-1.076797525650.3224305647490.343910743920.0871062332042-0.07428295916420.500321780808-0.04667290077720.3237044207588.2025707321844.42553695959.79550182791
86.029170295690.505001494249-2.508817560752.0014528715-1.087918490266.35886662849-0.1181451213710.321451724781-1.430333158850.144186838587-0.0654488554450.3550522040640.476239609349-0.8018228514280.2031111951850.446843284296-0.02248974803550.06377648187170.3760994922540.04457061976160.39457923306411.773834045717.677722720925.4143848389
93.459409082492.87266075395-0.9758274003214.89462402419-0.9619287006322.61066054143-0.028562940133-0.56784045171-0.4038293872150.502408671381-0.0131028161132-0.6545278618860.455714982234-0.00057358563787-0.02628285158820.2931202729040.05281270688020.02499699397130.3128456259880.05374991523360.29037828534820.411363323425.716500564726.9407207048
105.72568982986-0.0030255848685-0.9539567903952.98371259742-0.6976154555070.870891506671-0.424724028201-0.6010579565910.06849498153290.4568188944650.2928551091350.127058644349-0.1734068010790.1157666818720.06154277458310.3334081214410.0500729539195-0.04027742714890.228254996476-0.05685401714870.24131371186817.321696827631.170525492527.8376562787
113.243869433732.93831432925-0.9207660836843.66619234125-0.2931298418423.806443993780.00289585890303-0.112741778284-0.569592152052-0.122718456602-0.0815284157519-0.4179475391650.8602391296530.3988014249250.3663194171450.3186652591170.02959086405370.0611358952920.243073385424-0.01095084948730.35465987938923.167635352521.167460560118.6625007237
124.78415390128-0.845657888295-2.741747820260.977708366346-0.9478034244937.37153609725-0.7386598771540.662137084381-1.09415461782-0.9668645179730.395930468672-0.4224854924111.27006052324-0.1429895823290.3229531078880.508489421273-0.0002063531994490.1096040129530.396861329301-0.09642006727960.54677899437816.024562831118.92507269912.3850157814
132.35080253148-0.1905494241570.08031697866192.34929143812-1.810835987234.3962190042-0.4035353601240.5831312999030.02315113296240.113429784220.2133053146430.109365692124-0.349223563791-0.6613461907710.05700000459390.2565085042960.0667297887534-0.05991999854120.382764296286-0.04126584030250.23917766666710.635697136440.011389286512.0735948567
144.22750269495-1.6188598756-0.1240062200323.27767279628-0.868853087493.52400968847-0.1263902613271.0948027343-0.0527845864824-0.6855563993050.2009987815890.6500317456650.122330427994-0.5020958823590.1713075272280.3598270054720.0469538984194-0.06039713970550.583816836917-0.1681580794720.200749156711.457738580734.6439055718-1.31104508439
151.28787426162-0.2421924102470.5490101879540.791235166972-1.207901479892.997254355880.08497257692570.796120043895-0.49700196178-1.37128348595-0.0457166810476-0.2030996229481.213938581240.124166244127-0.2389344831030.7827125397020.009941490482160.005333788534750.814601583649-0.1714742552910.32989052752715.626824366528.505174797-8.41617822624
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 234 through 288 )AA234 - 2881 - 55
22chain 'A' and (resid 289 through 340 )AA289 - 34056 - 107
33chain 'A' and (resid 341 through 433 )AA341 - 433108 - 200
44chain 'A' and (resid 434 through 506 )AA434 - 506201 - 273
55chain 'B' and (resid 234 through 289 )BC234 - 2891 - 56
66chain 'B' and (resid 290 through 311 )BC290 - 31157 - 78
77chain 'B' and (resid 312 through 340 )BC312 - 34079 - 107
88chain 'B' and (resid 341 through 363 )BC341 - 363108 - 130
99chain 'B' and (resid 364 through 377 )BC364 - 377131 - 144
1010chain 'B' and (resid 378 through 400 )BC378 - 400145 - 167
1111chain 'B' and (resid 401 through 419 )BC401 - 419168 - 186
1212chain 'B' and (resid 420 through 432 )BC420 - 432187 - 199
1313chain 'B' and (resid 433 through 456 )BC433 - 456200 - 223
1414chain 'B' and (resid 457 through 484 )BC457 - 484224 - 251
1515chain 'B' and (resid 485 through 506 )BC485 - 506252 - 273

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