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

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Basic information

Entry
Database: PDB / ID: 4gbz
TitleThe structure of the MFS (major facilitator superfamily) proton:xylose symporter XylE bound to 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
beta-D-glucopyranose / D-xylose-proton symporter
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.894 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 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 1.3Feb 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)55,0486
Polymers53,6431
Non-polymers1,4065
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.036, 95.036, 168.566
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) / Gene: xylE, b4031, JW3991 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AGF4
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG 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


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.55 Å3/Da / Density % sol: 65.33 %
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: 0.9789 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 26, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.89→40 Å / Num. all: 17911 / Num. obs: 17572 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.9→3 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 / Resolution: 2.894→38.524 Å / SU ML: 0.56 / σ(F): 1.34 / Phase error: 30.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2888 898 5.12 %
Rwork0.2468 --
obs0.2489 17545 98.06 %
all-17891 -
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.668 Å2 / ksol: 0.332 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--14.8319 Å2-0 Å20 Å2
2---14.8319 Å2-0 Å2
3---43.5163 Å2
Refinement stepCycle: LAST / Resolution: 2.894→38.524 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3579 0 96 2 3677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093768
X-RAY DIFFRACTIONf_angle_d1.2075129
X-RAY DIFFRACTIONf_dihedral_angle_d18.4721304
X-RAY DIFFRACTIONf_chiral_restr0.078609
X-RAY DIFFRACTIONf_plane_restr0.005617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8944-3.07570.43261780.3862661X-RAY DIFFRACTION97
3.0757-3.3130.35511440.30242740X-RAY DIFFRACTION99
3.313-3.64620.28271540.23212759X-RAY DIFFRACTION99
3.6462-4.17330.28941460.20672774X-RAY DIFFRACTION99
4.1733-5.25580.26081320.21322811X-RAY DIFFRACTION98
5.2558-38.52730.27151440.26332902X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -20.195 Å / Origin y: 25.5829 Å / Origin z: -3.6462 Å
111213212223313233
T0.6674 Å20.096 Å2-0.0039 Å2-0.4939 Å2-0.0076 Å2--0.5408 Å2
L3.6199 °2-0.6536 °20.791 °2-1.8823 °2-0.4805 °2--1.7496 °2
S-0.2288 Å °-0.3092 Å °0.1106 Å °0.3043 Å °0.2955 Å °0.394 Å °-0.1369 Å °-0.111 Å °-0.1001 Å °
Refinement TLS groupSelection details: all

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