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- PDB-4gc0: The structure of the MFS (major facilitator superfamily) proton:x... -

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Basic information

Entry
Database: PDB / ID: 4gc0
TitleThe structure of the MFS (major facilitator superfamily) proton:xylose symporter XylE bound to 6-bromo-6-deoxy-D-glucose
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. / MFS general substrate transporter like domains / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Sugar transporter, conserved site / Growth Hormone; Chain: A; ...: / : / Sugar/inositol transporter / Sugar transport proteins signature 2. / Sugar transport proteins signature 1. / MFS general substrate transporter like domains / Major facilitator, sugar transporter-like / Sugar (and other) transporter / Sugar transporter, conserved site / 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
6-bromo-6-deoxy-beta-D-glucopyranose / D-xylose-proton symporter
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYan, N. / Sun, L.F. / Zeng, X. / Yan, C.Y.
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 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._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 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)55,1116
Polymers53,6431
Non-polymers1,4695
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.171, 95.171, 171.668
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


Mass: 53642.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: xylE, b4031, JW3991 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AGF4
#2: Sugar ChemComp-6BG / 6-bromo-6-deoxy-beta-D-glucopyranose / 6-bromo-6-deoxy-beta-D-glucose / 6-bromo-6-deoxy-D-glucose / 6-bromo-6-deoxy-glucose


Type: D-saccharide, beta linking / Mass: 243.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11BrO5
IdentifierTypeProgram
b-D-Glcp6bromoIUPAC CARBOHYDRATE SYMBOLPDB-CARE 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


Mass: 18.015 Da / Num. of mol.: 7 / 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: 3.62 Å3/Da / Density % sol: 66.05 %
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: SSRF / Beamline: BL17U / Wavelength: 0.9196 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 5, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9196 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. all: 25081 / Num. obs: 24981 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.6→2.69 Å / % possible all: 97.9

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GBY

4gby


Resolution: 2.6→39.123 Å / SU ML: 0.28 / σ(F): 1.12 / Phase error: 28.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2464 1241 4.98 %RANDOM
Rwork0.2271 ---
all0.2281 25021 --
obs0.2281 24914 99.57 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.919 Å2 / ksol: 0.343 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--18.736 Å2-0 Å20 Å2
2---18.736 Å2-0 Å2
3---24.0673 Å2
Refinement stepCycle: LAST / Resolution: 2.6→39.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3625 0 96 7 3728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123816
X-RAY DIFFRACTIONf_angle_d1.3245187
X-RAY DIFFRACTIONf_dihedral_angle_d17.5541337
X-RAY DIFFRACTIONf_chiral_restr0.083609
X-RAY DIFFRACTIONf_plane_restr0.009625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.65560.35531390.30742679X-RAY DIFFRACTION96
2.6556-2.71730.30171210.2982764X-RAY DIFFRACTION100
2.7173-2.78530.35181280.28542780X-RAY DIFFRACTION100
2.7853-2.86050.28761350.26322755X-RAY DIFFRACTION100
2.8605-2.94470.27851230.26452766X-RAY DIFFRACTION100
2.9447-3.03970.33141560.25712752X-RAY DIFFRACTION100
3.0397-3.14830.27141170.26132761X-RAY DIFFRACTION100
3.1483-3.27430.31841700.25552748X-RAY DIFFRACTION100
3.2743-3.42320.22941390.23272758X-RAY DIFFRACTION100
3.4232-3.60360.2361660.22262708X-RAY DIFFRACTION100
3.6036-3.82920.2311550.21962748X-RAY DIFFRACTION100
3.8292-4.12450.21411550.21622770X-RAY DIFFRACTION100
4.1245-4.5390.2071550.18822734X-RAY DIFFRACTION100
4.539-5.19460.23051680.19352728X-RAY DIFFRACTION100
5.1946-6.53960.2581510.25352741X-RAY DIFFRACTION100
6.5396-39.12750.24261240.21732695X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -27.2331 Å / Origin y: 21.9288 Å / Origin z: -3.9812 Å
111213212223313233
T0.5767 Å20.0811 Å20.0035 Å2-0.4871 Å20.0054 Å2--0.4825 Å2
L2.5783 °2-0.3198 °2-0.7292 °2-2.0187 °20.2669 °2--1.59 °2
S-0.1941 Å °-0.2515 Å °-0.1865 Å °0.2777 Å °0.1943 Å °-0.2985 Å °0.1114 Å °0.1199 Å °-0.0294 Å °
Refinement TLS groupSelection details: all

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