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- PDB-1fx8: CRYSTAL STRUCTURE OF THE E. COLI GLYCEROL FACILITATOR (GLPF) WITH... -

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Basic information

Entry
Database: PDB / ID: 1fx8
TitleCRYSTAL STRUCTURE OF THE E. COLI GLYCEROL FACILITATOR (GLPF) WITH SUBSTRATE GLYCEROL
ComponentsGLYCEROL UPTAKE FACILITATOR PROTEIN
KeywordsMEMBRANE PROTEIN / glycerol-conducting membrane channel protein
Function / homology
Function and homology information


glycerol transmembrane transporter activity / glycerol channel activity / glycerol transmembrane transport / cellular response to mercury ion / membrane => GO:0016020 / channel activity / metal ion binding / plasma membrane
Similarity search - Function
: / Glycerol uptake facilitator protein / Glycerol uptake facilitator protein. / Major intrinsic protein, conserved site / MIP family signature. / Major intrinsic protein / Major intrinsic protein / Aquaporin-like / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Glycerol uptake facilitator protein / Glycerol uptake facilitator protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsFu, D. / Libson, A. / Miercke, L.J.W. / Weitzman, C. / Nollert, P. / Stroud, R.M.
CitationJournal: Science / Year: 2000
Title: Structure of a glycerol-conducting channel and the basis for its selectivity.
Authors: Fu, D. / Libson, A. / Miercke, L.J. / Weitzman, C. / Nollert, P. / Krucinski, J. / Stroud, R.M.
History
DepositionSep 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 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 1.4Feb 7, 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

Downloads & links

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Assembly

Deposited unit
A: GLYCEROL UPTAKE FACILITATOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9537
Polymers29,8001
Non-polymers1,1536
Water2,000111
1
A: GLYCEROL UPTAKE FACILITATOR PROTEIN
hetero molecules

A: GLYCEROL UPTAKE FACILITATOR PROTEIN
hetero molecules

A: GLYCEROL UPTAKE FACILITATOR PROTEIN
hetero molecules

A: GLYCEROL UPTAKE FACILITATOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,81328
Polymers119,1994
Non-polymers4,61424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area17560 Å2
ΔGint-144 kcal/mol
Surface area36340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)96.760, 96.760, 184.322
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-300-

HOH

21A-301-

HOH

31A-302-

HOH

41A-303-

HOH

DetailsThe biological assembly is a tetramer generated by a crystallographic four-fold axis

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Components

#1: Protein GLYCEROL UPTAKE FACILITATOR PROTEIN / GLPF


Mass: 29799.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P11244, UniProt: P0AER0*PLUS
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.9
Details: GLPF at 15-20 mg/ml, 28%(w/v) PEG2K, 100mM Bicine, 15% (v/v) glycerol, 35mM n-octyl-beta-D-glucoside, 300mM MgCl2, 5mM DTT, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115-20 mg/mlprotein11
228 %(w/v)PEG200012
3100 mMbicine12
415 %(v/v)glycerol12
535 mMn-octyl-beta-D-glucoside12
6300 mM12MgCl2
75 mMdithiothreitol12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1
DetectorType: ADSC QUANTUM / Detector: CCD / Date: Sep 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 19141 / Num. obs: 19141 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.26 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 15.8
Reflection shellHighest resolution: 2.2 Å / Rmerge(I) obs: 0.393 / % possible all: 57.7
Reflection
*PLUS
Num. measured all: 139069
Reflection shell
*PLUS
% possible obs: 57.7 % / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
SHARPphasing
CNSrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2.2→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1966 -random
Rwork0.197 ---
all0.197 18716 --
obs0.197 18716 82.8 %-
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1895 0 78 111 2084
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å / σ(F): 0
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28 Å2
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.2

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