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- PDB-9o5f: Crystal Structure of EgtUC binding domain double mutant I243P T27... -

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Basic information

Entry
Database: PDB / ID: 9o5f
TitleCrystal Structure of EgtUC binding domain double mutant I243P 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
CITRATE ANION / Chem-LW8 / Ergothioneine transporter EgtUBC
Similarity search - Component
Biological speciesStreptococcus pneumoniae D39 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 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
DepositionApr 10, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2026Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5688
Polymers31,0081
Non-polymers5597
Water7,710428
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.851, 87.851, 207.639
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-604-

CL

21A-748-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ergothioneine transporter EgtUC


Mass: 31008.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae D39 (bacteria)
Gene: egtUBC, proWX, SPD_1642 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2ZQB9

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Non-polymers , 5 types, 435 molecules

#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.: 1 / Source method: obtained synthetically / Formula: C9H16N3O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.23 Å3/Da / Density % sol: 61.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Sodium Citrate pH 5.6 1.2 -1.8 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 PILATUS3 2M / Detector: PIXEL / Date: Apr 4, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.36→80.91 Å / Num. obs: 85513 / % possible obs: 99.1 % / Redundancy: 12.7 % / Biso Wilson estimate: 16.33 Å2 / CC1/2: 1 / Rpim(I) all: 0.02 / Rrim(I) all: 0.072 / Rsym value: 0.069 / Net I/σ(I): 23.8
Reflection shellResolution: 1.36→1.39 Å / Redundancy: 9.1 % / Rmerge(I) obs: 1.975 / Num. unique obs: 4041 / CC1/2: 0.425 / Rpim(I) all: 0.632 / Rsym value: 1.866 / % possible all: 94.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→80.91 Å / SU ML: 0.1466 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.3366
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1673 4312 5.06 %
Rwork0.1442 80963 -
obs0.1453 85275 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.42 Å2
Refinement stepCycle: LAST / Resolution: 1.36→80.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2163 0 33 428 2624
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00852290
X-RAY DIFFRACTIONf_angle_d1.05383111
X-RAY DIFFRACTIONf_chiral_restr0.0715340
X-RAY DIFFRACTIONf_plane_restr0.0087415
X-RAY DIFFRACTIONf_dihedral_angle_d00
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.380.35131340.31752466X-RAY DIFFRACTION92.04
1.38-1.40.29691360.29722646X-RAY DIFFRACTION97.41
1.4-1.410.28381560.27932663X-RAY DIFFRACTION99.79
1.41-1.430.27371480.25792686X-RAY DIFFRACTION99.89
1.43-1.450.26741420.24492688X-RAY DIFFRACTION99.96
1.45-1.470.22591370.23362720X-RAY DIFFRACTION99.97
1.47-1.490.23261340.22312703X-RAY DIFFRACTION100
1.49-1.510.24251610.21212693X-RAY DIFFRACTION99.86
1.51-1.540.22761490.20142687X-RAY DIFFRACTION99.89
1.54-1.560.21311460.18832694X-RAY DIFFRACTION99.96
1.56-1.590.18551260.18712729X-RAY DIFFRACTION99.9
1.59-1.620.1951430.16922691X-RAY DIFFRACTION99.96
1.62-1.650.19281390.172697X-RAY DIFFRACTION99.93
1.65-1.680.20341420.16082749X-RAY DIFFRACTION99.97
1.68-1.720.16651540.15632667X-RAY DIFFRACTION100
1.72-1.760.1771440.15222739X-RAY DIFFRACTION99.86
1.76-1.80.17671460.15212714X-RAY DIFFRACTION99.9
1.8-1.850.17831520.15922690X-RAY DIFFRACTION99.89
1.85-1.910.17271550.16172725X-RAY DIFFRACTION99.76
1.91-1.970.17991430.14682695X-RAY DIFFRACTION99.47
1.97-2.040.17611350.14232727X-RAY DIFFRACTION99.38
2.04-2.120.16161460.13332705X-RAY DIFFRACTION99.34
2.12-2.220.16081550.12962721X-RAY DIFFRACTION99.31
2.22-2.330.16421050.12552188X-RAY DIFFRACTION79.43
2.33-2.480.15461520.12462750X-RAY DIFFRACTION99.93
2.48-2.670.15061460.13432756X-RAY DIFFRACTION99.76
2.67-2.940.17391610.13622761X-RAY DIFFRACTION99.8
2.94-3.360.17571400.13352792X-RAY DIFFRACTION99.83
3.36-4.240.11871340.10072832X-RAY DIFFRACTION99.83
4.24-80.910.12851510.13052989X-RAY DIFFRACTION99.81
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)
15.188718310433.83484805688-6.870082122865.78220639253-5.843055109029.21101900441-0.241127259513-0.620516778264-0.289819185260.160635468732-0.0839706830420.007132956080820.2637951964140.1942677724520.3121134383730.1338090569130.03659723777190.02946113613710.3543073433260.04027909712610.17231996440631.353082201-3.473850917872.98781469773
21.151435960150.22264090195-0.1464164053821.09968467579-0.02481543817451.84543949491-0.0480527910169-0.396898743533-0.1149519138820.1316274975750.0003350769341780.02169522333830.0561728070754-0.04788094509550.05096163891920.09822223349650.03452621282460.01565032093570.2671238905750.01571475931350.14601529822832.7230962125-0.120664926968-1.58059062828
32.405979748930.1739163303360.4680749092971.25982900802-0.1135692923831.90797475466-0.0396689169647-0.05769672138440.04708211281-0.04286838748190.03816705282410.133182656462-0.0665948924564-0.276013917330.004038489053320.08951786002680.0367350571033-0.001609166155720.205899064047-0.01732423579770.13285870310422.28367817548.42682486408-12.8757144464
41.49579777622-0.07642802018470.3183554801771.66567887423-0.5119043453042.2831191921-0.03524763129080.0997645606370.163822127293-0.0687767968747-0.0469678280839-0.0988980170555-0.1895353974850.07520590243390.05659553032890.122466015569-0.00311752046548-0.0007304899996720.1199866383830.01401858488830.14561712391142.703976621514.3840221483-24.7882868988
53.90351355421-0.623403583042-0.005335968345672.23517292604-1.342026095311.7750621155-0.147951384794-0.2012671660150.4820551836680.055859098097-0.0182725621846-0.179335603849-0.286889015943-0.03311684371390.1307981385240.1650160841590.0161502830608-0.02059899943580.0946313174872-0.04883284532610.1810550497138.301616993319.1947629477-17.413183829
62.582526985170.41329314309-1.114026814422.38806216401-0.7314558064832.4732060509-0.0848019949667-0.509066244271-0.06347133999960.1744253713610.02027152571770.160485794355-0.0396721581457-0.3053758239870.03949984407740.1249728633040.0581006291660.009890291954520.392007935926-0.001081343926920.17432779019622.68609611764.56463498651.77560476275
71.65758031862-1.1555533142-1.524989710034.301017180930.3238442959766.58259172933-0.17744243022-0.7734986589870.4919981150010.381238865166-0.0504694659791-0.281153062133-0.3577140848770.2499116004110.1802949262660.183886103323-0.00255705076344-0.07451119581890.357962628415-0.09331888703480.21742808685239.98880295614.30114199414.49390945476
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 232 through 244 )232 - 2442 - 14
22chain 'A' and (resid 245 through 288 )245 - 28815 - 58
33chain 'A' and (resid 289 through 340 )289 - 34059 - 110
44chain 'A' and (resid 341 through 422 )341 - 422111 - 192
55chain 'A' and (resid 423 through 444 )423 - 444193 - 214
66chain 'A' and (resid 445 through 472 )445 - 472215 - 242
77chain 'A' and (resid 473 through 506 )473 - 506243 - 276

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