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- PDB-7txl: Crystal structure of EgtU solute binding domain from Streptococcu... -

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Basic information

Entry
Database: PDB / ID: 7txl
TitleCrystal structure of EgtU solute binding domain from Streptococcus pneumoniae D39 in complex with L-ergothioneine
ComponentsCholine transporter (Glycine betaine transport system permease protein)
KeywordsTRANSPORT PROTEIN / EGT / Soluble binding protein / SBP / ABC transporter
Function / homology
Function and homology information


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 / Choline transporter (Glycine betaine transport system permease protein)
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsZhang, Y. / 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)R35 GM118157 United States
CitationJournal: Nat Commun / Year: 2022
Title: Discovery and structure of a widespread bacterial ABC transporter specific for ergothioneine.
Authors: Zhang, Y. / Gonzalez-Gutierrez, G. / Legg, K.A. / Walsh, B.J.C. / Pis Diez, C.M. / Edmonds, K.A. / Giedroc, D.P.
History
DepositionFeb 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 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: Choline transporter (Glycine betaine transport system permease protein)
B: Choline transporter (Glycine betaine transport system permease protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6595
Polymers62,1372
Non-polymers5233
Water2,504139
1
A: Choline transporter (Glycine betaine transport system permease protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3613
Polymers31,0681
Non-polymers2922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Choline transporter (Glycine betaine transport system permease protein)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2992
Polymers31,0681
Non-polymers2301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.868, 128.743, 207.540
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
11B-764-

HOH

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Components

#1: Protein Choline transporter (Glycine betaine transport system permease protein)


Mass: 31068.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466) (bacteria)
Strain: D39 / NCTC 7466 / Gene: proWX, SPD_1642 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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 / Ergothioneine


Mass: 230.307 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
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: 3.22 Å3/Da / Density % sol: 61.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 1.6 M Sodium citrate tribasic dihydrate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.07216 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07216 Å / Relative weight: 1
ReflectionResolution: 2.44→43.86 Å / Num. obs: 29967 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 38.56 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.073 / Rrim(I) all: 0.195 / Rsym value: 0.167 / Net I/σ(I): 8.5
Reflection shellResolution: 2.44→2.54 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3349 / CC1/2: 0.714 / Rpim(I) all: 0.496 / Rrim(I) all: 1.282 / Rsym value: 1.086 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z7E

4z7e


Resolution: 2.44→43.86 Å / SU ML: 0.3261 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.047
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2477 1450 4.85 %
Rwork0.1957 28467 -
obs0.1981 29917 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.25 Å2
Refinement stepCycle: LAST / Resolution: 2.44→43.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4324 0 34 139 4497
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044433
X-RAY DIFFRACTIONf_angle_d0.60285988
X-RAY DIFFRACTIONf_chiral_restr0.0386667
X-RAY DIFFRACTIONf_plane_restr0.0047777
X-RAY DIFFRACTIONf_dihedral_angle_d00
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.44-2.530.36451320.2892810X-RAY DIFFRACTION99.56
2.53-2.630.35911340.27342817X-RAY DIFFRACTION99.56
2.63-2.750.34741420.25922850X-RAY DIFFRACTION99.8
2.75-2.890.30631430.24542795X-RAY DIFFRACTION99.86
2.89-3.070.33871560.24942804X-RAY DIFFRACTION99.8
3.07-3.310.27761670.22562829X-RAY DIFFRACTION99.97
3.31-3.640.2361300.19542869X-RAY DIFFRACTION99.83
3.64-4.170.20131440.1642857X-RAY DIFFRACTION99.87
4.17-5.250.18481590.14292851X-RAY DIFFRACTION99.9
5.26-43.860.20261430.16492985X-RAY DIFFRACTION99.71
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)
12.53731837525-0.7532218986370.09266578129033.0071140168-0.5155471028393.527827025150.0103034635744-0.06570981586440.1308701254770.434284133065-0.0909437771870.274774859166-0.473276118646-0.247195120630.08922874040950.4866951213660.08987902918060.0261571177150.267244799221-0.05920682910580.33760592812522.529278264247.049041892598.6381795236
22.273755282730.0472791447848-1.133796671253.98001896126-0.4021911947165.58508102426-0.04526686510840.2717081808970.0968563644764-0.15729504213-0.115968487961-0.613605005654-0.1965816019140.6640220625260.126827031450.322036003780.03430128985990.01270153506880.3867106028660.06326908264570.35639319605340.45832606143.031718677480.4662644179
31.93682837111-0.0718885385445-0.9381840086862.151031145520.4026979782284.33873637260.0760737751128-0.1579553046270.2443019934370.69848945419-0.137315364781-0.0870093616121-0.5100496159770.397818861468-0.04158614399930.64137155765-0.0280987127207-0.05644192577610.234415339556-0.03797263535560.38731671829731.433317510749.6405140037102.941756294
41.43983802320.1938466047591.032547672410.8784473328020.3306676077551.32821773727-0.1055428055460.596258517492-0.255263550059-0.283288221581-0.1114428192060.1589156060540.137654523309-0.2620243785280.1315856159080.3597340702370.04706395224290.04228054464390.539763452586-0.08079319730580.3464244721717.6830495613355.810463423352.2513702191
54.286066607440.3989708252890.3890615491612.61790706785-0.37182322944.02323124221-0.3979658716710.159216902434-0.445709017428-0.01510385969410.0707286706972-0.2728716823180.2920408887850.316400292210.2702325581040.3775066449480.08642671113720.1032427211170.3146084787840.006814281722740.33720593933219.310438863352.987674969763.9143338053
65.187657880180.6160203087310.4427476786421.819658332611.561387598813.88960846774-0.0673672179679-0.1820129615750.4426764251740.141374751929-0.0179504846595-0.0458499844952-0.65589448172-0.02510218530550.08182003001350.5086346850710.0827265322658-0.02576175422780.303767005021-0.008742833539710.33641460460911.744077080372.83155891776.8295851011
73.9756092561-3.13626063292-0.1762898379282.7352831986-0.3465073484324.0224555370.1083474606920.1651292922670.851922804961-0.469174015827-0.0341578920192-0.103086559114-1.63618051932-0.09364926510970.1892885659470.8529751117850.0789147806096-0.07844739054260.3764458687770.1355528897260.54298717276913.470713399577.863625960864.585845018
83.200110632230.01964762184020.2275457703371.541054944910.4307004346195.17499333742-0.08284605051220.7892291374660.0824221415918-0.422173310081-0.153510385603-0.178908478591-0.618889209330.05599968607790.1735603806440.3768476953280.01937711045610.01834277912770.4934969774610.02398609733820.349203136817.345749917662.36952154453.1024125148
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 432 )AA341 - 432110 - 201
33chain 'A' and (resid 433 through 506 )AA433 - 506202 - 275
44chain 'B' and (resid 233 through 284 )BD233 - 2841 - 52
55chain 'B' and (resid 285 through 340 )BD285 - 34053 - 108
66chain 'B' and (resid 341 through 419 )BD341 - 419109 - 187
77chain 'B' and (resid 420 through 432 )BD420 - 432188 - 200
88chain 'B' and (resid 433 through 506 )BD433 - 506201 - 274

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