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- PDB-9egi: Crystal Structure of EgtUC binding domain mutant T274G bound to L... -

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Basic information

Entry
Database: PDB / ID: 9egi
TitleCrystal Structure of EgtUC binding domain mutant T274G 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: 1.95 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
Citation
Journal: 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.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
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)62,5094
Polymers62,0492
Non-polymers4612
Water4,702261
1
A: Ergothioneine transporter EgtUC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2552
Polymers31,0241
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)31,2552
Polymers31,0241
Non-polymers2301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)120.153, 127.313, 206.655
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-824-

HOH

21B-807-

HOH

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Components

#1: Protein Ergothioneine transporter EgtUC


Mass: 31024.301 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.: 261 / 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: 3.18 Å3/Da / Density % sol: 61.32 %
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 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.95→51.94 Å / Num. obs: 33902 / % possible obs: 88 % / Redundancy: 6.3 % / Biso Wilson estimate: 34.78 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.046 / Rrim(I) all: 0.118 / Rsym value: 0.108 / Net I/σ(I): 8.8
Reflection shellResolution: 1.95→2.22 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1696 / CC1/2: 0.652 / Rpim(I) all: 0.489 / Rrim(I) all: 1.109 / Rsym value: 0.991

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→51.94 Å / SU ML: 0.2064 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.8544
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2434 1593 4.71 %
Rwork0.2005 32203 -
obs0.2025 33796 58.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.02 Å2
Refinement stepCycle: LAST / Resolution: 1.95→51.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4300 0 30 261 4591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00874406
X-RAY DIFFRACTIONf_angle_d1.08875953
X-RAY DIFFRACTIONf_chiral_restr0.0627661
X-RAY DIFFRACTIONf_plane_restr0.0071774
X-RAY DIFFRACTIONf_dihedral_angle_d8.1375591
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.010.316470.2856117X-RAY DIFFRACTION2.38
2.01-2.080.3128140.2993297X-RAY DIFFRACTION5.97
2.08-2.170.4102320.3091631X-RAY DIFFRACTION12.84
2.17-2.260.4359560.3131163X-RAY DIFFRACTION23.41
2.26-2.380.3121180.28152067X-RAY DIFFRACTION41.91
2.38-2.530.36031630.26943596X-RAY DIFFRACTION72.03
2.53-2.730.30872330.27354585X-RAY DIFFRACTION91.98
2.73-30.27062580.25794870X-RAY DIFFRACTION97.94
3-3.440.2992020.22314968X-RAY DIFFRACTION98.46
3.44-4.330.21832630.16724871X-RAY DIFFRACTION96.7
4.33-51.940.17852470.15145038X-RAY DIFFRACTION97.1
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)
11.92323684107-0.5146681553370.8927966937112.49911796431-0.6271669997063.97133906992-0.057905948522-0.00778251450650.05145186166460.27336298587-0.09529493399150.289571597704-0.409652459212-0.1762771832580.07689159947920.284756661520.1059056729420.008478033841440.170234123383-0.0487334397270.27605152069722.4233996069-17.0369144756-5.28146131446
21.62692598887-1.00090729699-1.379269768513.813539527780.9599193557295.87732167877-0.08653138452150.03030271290720.108784271212-0.0610872779629-0.100419401309-0.573747008756-0.03290870069841.001550467650.1505905173250.2630755127490.03775801618950.00996500117530.404585353540.1030077525090.29242338390339.7889022294-19.5724279062-22.9974332604
33.0574720751-0.390148166872-0.5562914914563.632435349130.374425780254.14196669216-0.0733929259962-0.3884386464560.2352313591380.632069819162-0.00900968497789-0.067128463251-0.5564665686920.338421679440.01894032154270.458599965334-0.0104156686017-0.01568998475320.21723622587-0.02409572796850.19480884363230.7224150787-15.70821147373.53298134382
42.32501002698-0.679184718295-1.171347157442.522098762770.4131613021153.65990478228-0.2473562848120.822699104766-0.396123556073-0.387809801036-0.06549597407930.2254005121510.131852724833-0.1915055545720.2651155260840.2874482134960.03480017790590.01099320858230.568484829115-0.114566716520.280396312727.60658016288-8.37225601508-50.5058662796
51.633862650790.03796433777250.9032653823042.30412526778-0.5069591667423.58493096134-0.4058934589790.252362752162-0.5152195300520.08669547984910.115692328709-0.2403098662080.1183353660760.4870135007760.1412034077720.2442596463520.1308950990590.1193088455650.36494337517-0.0009977378508430.34746230104120.5910368812-10.5556457792-39.1740275116
64.68656685565-0.1668315472930.04892968719292.602013291291.052635048983.37394318315-0.193457850531-0.1178407783920.6654853076010.3291709925340.0774817284797-0.0799202568854-0.4468106669230.1981196154870.07024459830460.305950097340.0426302848247-0.06276114572490.2112822887260.006600164517810.27430835393511.60951030338.7272228425-27.2188585782
73.18891884-0.13029634319-0.1780961831572.467081475350.7915171907693.44871983601-0.09137441383060.8655453947090.254397037233-0.606832747024-0.0738379545394-0.204605980224-0.5854717956240.1955298480640.1506910692370.392853809271-0.0301669021140.01537801589160.5808154619920.1368000080320.27069636074916.62997530990.624374743421-48.9947367075
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 232 through 340 )AA232 - 3401 - 109
22chain 'A' and (resid 341 through 444 )AA341 - 444110 - 213
33chain 'A' and (resid 445 through 506 )AA445 - 506214 - 275
44chain 'B' and (resid 235 through 288 )BC235 - 2881 - 54
55chain 'B' and (resid 289 through 340 )BC289 - 34055 - 106
66chain 'B' and (resid 341 through 422 )BC341 - 422107 - 188
77chain 'B' and (resid 423 through 506 )BC423 - 506189 - 272

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