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- PDB-8zoj: The crystal structure of YegTK267A from the Nucleoside: H+ Sympor... -

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Basic information

Entry
Database: PDB / ID: 8zoj
TitleThe crystal structure of YegTK267A from the Nucleoside: H+ Symporter Family
ComponentsPutative nucleoside transporter YegT
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


cytidine transmembrane transporter activity / uridine transmembrane transporter activity / plasma membrane
Similarity search - Function
Nucleoside:H+ symporter / Nucleoside H+ symporter / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Putative nucleoside transporter YegT
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.913 Å
AuthorsXiao, Q.J. / Deng, D.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Mechanistic insights into proton-coupled substrate translocation of nucleoside proton symporters.
Authors: Xiao, Q. / Chen, X. / Wang, C. / He, Y. / Deng, D. / Sun, B.
History
DepositionMay 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Putative nucleoside transporter YegT
A: Putative nucleoside transporter YegT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,87011
Polymers94,6612
Non-polymers3,2099
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-23 kcal/mol
Surface area34940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.769, 58.212, 105.076
Angle α, β, γ (deg.)77.85, 81.30, 68.46
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Putative nucleoside transporter YegT


Mass: 47330.691 Da / Num. of mol.: 2 / Mutation: K267A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Gene: yegT, b2098, JW2085 / Production host: Escherichia coli (E. coli) / References: UniProt: P76417
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C21H40O4
Has ligand of interestN
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: 2.5 Å3/Da / Density % sol: 50.83 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.1 M MES (pH=5.8), 0.1 M Li2SO4, 0.1 M glycine, and 26% PEG550MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.91→50 Å / Num. obs: 20090 / % possible obs: 98.1 % / Redundancy: 3.43 % / CC1/2: 0.996 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.111 / Net I/σ(I): 4.03
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.91-3.091.59410060.1270.9291
3.09-3.30.60410150.3070.7121
3.3-3.560.4818610.690.6811
3.56-3.90.2287880.9290.3231
3.9-4.360.1367040.9560.1931
4.36-5.020.0835960.9850.1181
5.02-6.130.0895140.9790.1261
6.13-8.590.0313580.9970.0431
8.59-300.0291820.9960.041

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.913→39.139 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2619 1967 10.01 %
Rwork0.2413 --
obs0.2434 19644 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.913→39.139 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6199 0 165 0 6364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116550
X-RAY DIFFRACTIONf_angle_d1.3788851
X-RAY DIFFRACTIONf_dihedral_angle_d22.9482238
X-RAY DIFFRACTIONf_chiral_restr0.068978
X-RAY DIFFRACTIONf_plane_restr0.0081067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9132-2.9860.31891310.31891216X-RAY DIFFRACTION96
2.986-3.06670.32231530.28791286X-RAY DIFFRACTION97
3.0667-3.15690.34581240.28771245X-RAY DIFFRACTION99
3.1569-3.25880.33651520.3011263X-RAY DIFFRACTION97
3.2588-3.37520.35631320.27231265X-RAY DIFFRACTION98
3.3752-3.51020.3041500.26041276X-RAY DIFFRACTION98
3.5102-3.66990.26691380.24321254X-RAY DIFFRACTION98
3.6699-3.86320.24181350.24081314X-RAY DIFFRACTION98
3.8632-4.1050.25821430.23151232X-RAY DIFFRACTION99
4.105-4.42160.23461480.22251295X-RAY DIFFRACTION98
4.4216-4.86580.26031350.19791238X-RAY DIFFRACTION98
4.8658-5.56820.24511390.24351265X-RAY DIFFRACTION99
5.5682-7.00870.25681440.26491282X-RAY DIFFRACTION98
7.0087-39.1390.21261430.21261246X-RAY DIFFRACTION97
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)
10.50350.7665-1.10670.1632-0.0970.9953-0.02980.06460.06050.0149-0.08010.540.12730.057300.2844-0.0461-0.03770.3548-0.00540.35497.96088.825256.7476
20.0280.2966-0.43571.33390.04211.09850.1111-0.00460.06670.2124-0.08340.15840.13060.052600.3376-0.0360.03330.3731-0.01250.459612.79076.509466.1901
30.09660.3640.46550.33780.00280.84420.04120.03350.05790.3558-0.08470.1058-0.0282-0.0174-00.6657-0.13760.12650.5381-0.05710.503510.48819.595178.6519
40.26820.05580.3803-0.1079-0.12330.25320.3525-0.16990.44220.2139-0.42521.0582-0.0867-0.0778-00.5933-0.11810.23760.4796-0.04590.47336.89421.536482.3739
52.00022.0011.99921.99991.99885.6738-0.2035-0.1620.19290.0638-0.03790.1437-0.0730.14210.06841.6247-0.11180.24470.74710.45671.23928.8196-8.131492.7548
60.2947-0.47830.04060.2804-0.66161.12020.1066-0.0063-0.1046-0.01330.03050.1931-0.1101-0.0114-00.28360.0617-0.05280.39570.02270.33949.21086.074828.1018
70.3696-0.09930.49790.09170.0937-0.0835-0.1178-0.11930.0633-0.9450.06990.43790.002-0.051700.6294-0.046-0.00090.45190.03780.5415.128810.655338.9127
80.51-0.07160.8959-0.01560.53790.80970.0207-0.0532-0.1442-0.2708-0.0981-0.0444-0.3366-0.083600.3510.02920.0420.41520.02750.460512.764513.59128.0081
9-0.44190.37320.15751.57280.52750.9094-0.0566-0.16460.0576-0.204-0.05420.17520.0317-0.032800.2970.0725-0.06970.3897-0.0230.43019.75657.06922.1398
10-0.2041-0.78870.17030.0591-0.2820.23950.0877-0.16140.415-0.6148-0.3774-0.25240.1935-0.0572-00.65740.1157-0.07680.38240.03690.559718.65718.36467.3086
110.04080.4021-0.40480.236-0.85240.69350.0490.10730.0852-0.5674-0.04640.1114-0.1868-0.02200.68550.0685-0.1230.5221-0.02080.604312.193510.714710.5589
12-0.08-0.4548-0.01060.12890.92020.4950.2413-0.3366-0.2504-1.014-0.37930.27170.2207-0.147100.56040.165-0.19150.3988-0.12950.49294.3236-4.83798.9133
136.25582.0003-2.27142-3.02072.53880.23450.0573-0.23080.3236-0.1519-0.41330.015-0.0514-0.03541.7986-0.17120.45240.67970.36690.35687.384925.0603-4.3295
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 90 )
2X-RAY DIFFRACTION2chain 'B' and (resid 91 through 269 )
3X-RAY DIFFRACTION3chain 'B' and (resid 270 through 364 )
4X-RAY DIFFRACTION4chain 'B' and (resid 365 through 401 )
5X-RAY DIFFRACTION5chain 'B' and (resid 402 through 403 )
6X-RAY DIFFRACTION6chain 'A' and (resid 1 through 60 )
7X-RAY DIFFRACTION7chain 'A' and (resid 61 through 90 )
8X-RAY DIFFRACTION8chain 'A' and (resid 91 through 146 )
9X-RAY DIFFRACTION9chain 'A' and (resid 147 through 243 )
10X-RAY DIFFRACTION10chain 'A' and (resid 244 through 291 )
11X-RAY DIFFRACTION11chain 'A' and (resid 292 through 347 )
12X-RAY DIFFRACTION12chain 'A' and (resid 348 through 401 )
13X-RAY DIFFRACTION13chain 'A' and (resid 402 through 403 )

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