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

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Basic information

Entry
Database: PDB / ID: 1ldi
TitleCRYSTAL STRUCTURE OF THE E. COLI GLYCEROL FACILITATOR (GLPF) WITHOUT SUBSTRATE GLYCEROL
ComponentsGlycerol uptake facilitator protein
KeywordsTRANSPORT 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 / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNollert, P. / Miercke, L.J.W. / O'Connell, J. / Stroud, R.M.
Citation
Journal: Science / Year: 2002
Title: Control of the selectivity of the aquaporin water channel family by global orientational tuning.
Authors: Tajkhorshid, E. / Nollert, P. / Jensen, M.O. / Miercke, L.J. / O'Connell, J. / Stroud, R.M. / Schulten, K.
#1: Journal: 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
DepositionApr 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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 1.4Aug 16, 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
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycerol uptake facilitator protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3853
Polymers29,8001
Non-polymers5852
Water1,11762
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)121,53812
Polymers119,1994
Non-polymers2,3398
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 area14670 Å2
ΔGint-139 kcal/mol
Surface area34360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)96.053, 96.053, 184.195
Angle α, β, γ (deg.)90.0, 90.0, 90.00
Int Tables number97
Space group name H-MI422
DetailsThe biological assembly is created by the crystallographic four-fold axis: -X+1, -Y+1, Z; -Y+1,X,Z; Y,-X+1,Z

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Components

#1: Protein Glycerol uptake facilitator protein / Aquaglyceroporin


Mass: 29799.842 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / 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.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 65.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: GLPF at 15-20 mg/ml, 100 mM Bicine, 28% (w/v) PEG 2000, 300mM MgCl2, 5 mMDTT, 15 % (v/v) xylose, 35 mM N-octyl-beta-D-glucoside, pH 9.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8.9 / 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: Jun 7, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 10918 / % possible obs: 87.5 % / Observed criterion σ(I): 0 / Redundancy: 5.949 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 14
Reflection shellHighest resolution: 2.7 Å / Rmerge(I) obs: 0.322 / % possible all: 83.2
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 30 Å / Num. measured all: 64951 / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
Rmerge(I) obs: 0.322

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FX8

1fx8


Resolution: 2.7→30 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1144 -RANDOM
Rwork0.229 ---
obs-10918 87.5 %-
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1895 0 40 62 1997
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.26
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 30 Å / Rfactor obs: 0.229 / Rfactor Rfree: 0.261 / Rfactor Rwork: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS

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