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- PDB-4gby: The structure of the MFS (major facilitator superfamily) proton:x... -

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Basic information

Entry
Database: PDB / ID: 4gby
TitleThe structure of the MFS (major facilitator superfamily) proton:xylose symporter XylE bound to D-xylose
ComponentsD-xylose-proton symporter
KeywordsTRANSPORT PROTEIN / MFS / D-xylose:proton symporter
Function / homology
Function and homology information


D-xylose:proton symporter activity / D-xylose transmembrane transport / transmembrane transporter activity / transmembrane transport / membrane / plasma membrane
Similarity search - Function
: / Sugar/inositol transporter / Sugar transport proteins signature 2. / Sugar transport proteins signature 1. / Major facilitator, sugar transporter-like / Sugar (and other) transporter / MFS general substrate transporter like domains / Sugar transporter, conserved site / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. ...: / Sugar/inositol transporter / Sugar transport proteins signature 2. / Sugar transport proteins signature 1. / Major facilitator, sugar transporter-like / Sugar (and other) transporter / MFS general substrate transporter like domains / Sugar transporter, conserved site / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Growth Hormone; Chain: A; / MFS transporter superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
beta-D-xylopyranose / D-xylose-proton symporter
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.808 Å
AuthorsSun, L.F. / Zeng, X. / Yan, C.Y. / Yan, N.
CitationJournal: Nature / Year: 2012
Title: Crystal structure of a bacterial homologue of glucose transporters GLUT1-4.
Authors: Sun, L. / Zeng, X. / Yan, C. / Sun, X. / Gong, X. / Rao, Y. / Yan, N.
History
DepositionJul 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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-proton symporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0186
Polymers53,6431
Non-polymers1,3765
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.290, 95.290, 168.181
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein D-xylose-proton symporter / D-xylose transporter


Mass: 53642.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: xylE, b4031, JW3991 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AGF4
#2: Sugar ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose / Xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Sugar
ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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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: 3.56 Å3/Da / Density % sol: 65.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.6
Details: 40 % (w/v) PEG400, 0.05 M Glycine pH 9.6 and 0.1 M LiCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 10, 2011
RadiationMonochromator: rotated-inclined double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.77→40 Å / Num. all: 20321 / Num. obs: 19996 / % possible obs: 98.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.77→2.87 Å / % possible all: 96.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.808→29.714 Å / SU ML: 0.49 / σ(F): 1.03 / Phase error: 24.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2736 1004 5.18 %RANDOM
Rwork0.2275 ---
obs0.2298 19517 99.69 %-
all-20268 --
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.506 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.4306 Å2-0 Å20 Å2
2---7.4306 Å2-0 Å2
3---14.8613 Å2
Refinement stepCycle: LAST / Resolution: 2.808→29.714 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3587 0 94 6 3687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013774
X-RAY DIFFRACTIONf_angle_d1.285137
X-RAY DIFFRACTIONf_dihedral_angle_d17.1211309
X-RAY DIFFRACTIONf_chiral_restr0.078608
X-RAY DIFFRACTIONf_plane_restr0.006620
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.808-2.88370.43041340.36442641X-RAY DIFFRACTION100
2.8837-2.96850.45641210.34562630X-RAY DIFFRACTION100
2.9685-3.06430.32391560.29882628X-RAY DIFFRACTION100
3.0643-3.17370.35211270.26542659X-RAY DIFFRACTION100
3.1737-3.30060.27361500.22752624X-RAY DIFFRACTION100
3.3006-3.45060.26041600.21442607X-RAY DIFFRACTION100
3.4506-3.63220.23261460.2062635X-RAY DIFFRACTION100
3.6322-3.85930.26681400.20432640X-RAY DIFFRACTION100
3.8593-4.15660.26071580.212601X-RAY DIFFRACTION100
4.1566-4.57350.25941570.20322614X-RAY DIFFRACTION100
4.5735-5.23220.2191380.19562646X-RAY DIFFRACTION100
5.2322-6.58020.2921550.24292594X-RAY DIFFRACTION99
6.5802-29.71590.27851200.23382588X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 20.1233 Å / Origin y: -25.7359 Å / Origin z: -3.5561 Å
111213212223313233
T0.3478 Å20.0561 Å20.0085 Å2-0.1803 Å20.0166 Å2--0.1997 Å2
L1.972 °20.0451 °2-0.4957 °2-1.1645 °20.1649 °2--1.741 °2
S-0.1018 Å °-0.1504 Å °0.0123 Å °0.1568 Å °0.1313 Å °-0.1721 Å °0.0854 Å °0.0839 Å °0.046 Å °
Refinement TLS groupSelection details: all

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