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- PDB-6n3i: Crystal structure of a double Trp XylE mutants (G58W/L315W) -

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Basic information

Entry
Database: PDB / ID: 6n3i
TitleCrystal structure of a double Trp XylE mutants (G58W/L315W)
ComponentsD-xylose transporter
KeywordsTRANSPORT PROTEIN / sugar transporter
Function / homology
Function and homology information


D-xylose:proton symporter activity / D-xylose transmembrane transport / 2-alkenal reductase [NAD(P)H] activity / symporter activity / transmembrane transporter activity / transmembrane transport / membrane / plasma membrane
Similarity search - Function
: / : / : / Sugar/inositol transporter / Sugar transport proteins signature 2. / MFS general substrate transporter like domains / Sugar transport proteins signature 1. / Sugar transporter, conserved site / Major facilitator, sugar transporter-like / Sugar (and other) transporter ...: / : / : / Sugar/inositol transporter / Sugar transport proteins signature 2. / MFS general substrate transporter like domains / Sugar transport proteins signature 1. / Sugar transporter, conserved site / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Growth Hormone; Chain: A; / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
D-xylose transporter / D-xylose-proton symporter
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.69 Å
AuthorsJiang, X. / Wu, J.P. / Yan, N.
CitationJournal: Cell Discov / Year: 2019
Title: Engineered XylE as a tool for mechanistic investigation and ligand discovery of the glucose transporters GLUTs.
Authors: Jiang, X. / Wu, J. / Ke, M. / Zhang, S. / Yuan, Y. / Lin, J.Y. / Yan, N.
History
DepositionNov 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-xylose transporter


Theoretical massNumber of molelcules
Total (without water)56,7711
Polymers56,7711
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area19560 Å2
Unit cell
Length a, b, c (Å)89.076, 95.482, 106.837
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein D-xylose transporter / D-xylose transporter XylE / D-xylose-proton symporter / Xylose-proton symport


Mass: 56770.914 Da / Num. of mol.: 1 / Mutation: G58W, L315W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: xylE, A6581_03910, A8C65_05810, A8G17_02365, A9R57_24335, ACU57_23655, AM266_00125, APT13_02355, ARC77_17295, AU473_00570, AUQ13_09605, AXA56_02835, BET08_27805, BHS87_22560, BIZ41_02050, BJJ90_ ...Gene: xylE, A6581_03910, A8C65_05810, A8G17_02365, A9R57_24335, ACU57_23655, AM266_00125, APT13_02355, ARC77_17295, AU473_00570, AUQ13_09605, AXA56_02835, BET08_27805, BHS87_22560, BIZ41_02050, BJJ90_24840, BTQ04_08325, BUE81_27360, BW690_24570, BWP17_09190, BZL31_21205, C4J69_17240, C5N07_20120, C9E25_05830, CR539_01970, CVH05_05200, DNQ41_01650, EC3234A_77c00210, ECs5014, EL75_4158, ERS085365_03771, ERS085383_01436, ERS085404_01231, ERS085416_00617, ERS139211_03640, ERS150873_01173, NCTC11022_04351, NCTC13127_06094, NCTC8500_05257, NCTC9010_04850, NCTC9037_04731, NCTC9045_05486, NCTC9058_02196, NCTC9060_03761, NCTC9062_03497, NCTC9110_04439, NCTC9701_04938, NCTC9969_04869, PGD_03203, RK56_017160, SAMEA3472067_03745, SAMEA3472080_00244, SAMEA3484427_03815, SAMEA3484429_02460, SAMEA3752557_02204, SAMEA3752559_00300, SAMEA3753093_02732, SAMEA3753106_03785, SAMEA3753300_00801, SAMEA3753391_00781, SAMEA3753397_01641
Production host: Escherichia coli (E. coli)
References: UniProt: C3SHS4, UniProt: P0AGF4*PLUS, 2-alkenal reductase [NAD(P)+]

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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: 4 Å3/Da / Density % sol: 69.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1 M NaCl, 0.1 M Li2SO4, 0.1 M MES pH6.5, 30% PEG400 (v/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.69→40 Å / Num. obs: 10052 / % possible obs: 98.3 % / Redundancy: 5.5 % / Net I/σ(I): 17.8
Reflection shellResolution: 3.7→3.83 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.4 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GBZ

4gbz


Resolution: 3.69→35.597 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3296 493 4.87 %
Rwork0.2911 --
obs0.293 10131 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.69→35.597 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3641 0 0 0 3641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063740
X-RAY DIFFRACTIONf_angle_d1.1535096
X-RAY DIFFRACTIONf_dihedral_angle_d15.7311268
X-RAY DIFFRACTIONf_chiral_restr0.041584
X-RAY DIFFRACTIONf_plane_restr0.005627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6899-4.06080.38721020.32272344X-RAY DIFFRACTION98
4.0608-4.64730.36321170.27342397X-RAY DIFFRACTION100
4.6473-5.85090.3331540.32532376X-RAY DIFFRACTION100
5.8509-35.59820.30031200.27412521X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 13.394 Å / Origin y: -15.4176 Å / Origin z: -2.9314 Å
111213212223313233
T0.8477 Å2-0.0536 Å2-0.0714 Å2-0.714 Å20.0023 Å2--0.8465 Å2
L0.3401 °2-0.511 °2-0.4912 °2--0.6844 °2-0.7973 °2--0.4658 °2
S-0.0837 Å °-0.2015 Å °0.4469 Å °0.0595 Å °-0.0685 Å °0.0576 Å °-0.0574 Å °0.1717 Å °-0.0009 Å °
Refinement TLS groupSelection details: all

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