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- PDB-1pw4: Crystal Structure of the Glycerol-3-Phosphate Transporter from E.Coli -

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Basic information

Entry
Database: PDB / ID: 1pw4
TitleCrystal Structure of the Glycerol-3-Phosphate Transporter from E.Coli
ComponentsGlycerol-3-phosphate transporter
KeywordsMEMBRANE PROTEIN / Glycerol-3-Phosphate / Transmembrane / Inner membrane / Transporter / Major facilitator superfamily / Secondary active membrane transporter
Function / homology
Function and homology information


glycerol-3-phosphate transmembrane transporter activity / organophosphate:phosphate antiporter activity / glycerol-phosphate:phosphate antiporter activity / glycerol-3-phosphate transmembrane transport / glycerol transmembrane transport / glycerol metabolic process / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Sugar phosphate transporter / Glycerol-3-phosphate transporter / Glycerate/sugar phosphate transporter, conserved site / glpT family of transporters signature. / MFS general substrate transporter like domains / Major facilitator superfamily / Major Facilitator Superfamily / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Growth Hormone; Chain: A; ...Sugar phosphate transporter / Glycerol-3-phosphate transporter / Glycerate/sugar phosphate transporter, conserved site / glpT family of transporters signature. / MFS general substrate transporter like domains / Major facilitator superfamily / Major Facilitator Superfamily / 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
Glycerol-3-phosphate transporter
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.3 Å
AuthorsHuang, Y. / Lemieux, M.J. / Song, J. / Auer, M. / Wang, D.N.
CitationJournal: Science / Year: 2003
Title: Structure and Mechanism of the Glycerol-3-Phosphate Transporter from Escherichia Coli
Authors: Huang, Y. / Lemieux, M.J. / Song, J. / Auer, M. / Wang, D.N.
History
DepositionJun 30, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycerol-3-phosphate transporter


Theoretical massNumber of molelcules
Total (without water)50,2441
Polymers50,2441
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.640, 97.640, 175.151
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsFunction as monomer, one molecule per asymmetric unit.

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Components

#1: Protein Glycerol-3-phosphate transporter / G-3-P transporter / G-3-P permease


Mass: 50243.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: glpT / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194
Keywords: T.C.2.A.1.4.3 from transporter protein database at UCSF
References: UniProt: P08194

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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: 4.79 Å3/Da / Density % sol: 74.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7
Details: 25% PEG2K MME, 20% Glycerol, 5% MPD, 0.1M Tris pH8.7, 1mM DTT, 5mM NaAc, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 mg/mlprotein11
25 mMdithiothreitol11

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2510.9789, 1.214
SYNCHROTRONAPS 19-ID20.9791
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDFeb 19, 2003
SBC-22CCDJun 28, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
21.2141
30.97911
ReflectionResolution: 3→30 Å / Num. all: 14944 / Num. obs: 14870 / % possible obs: 99.5 % / Observed criterion σ(F): 2.8 / Observed criterion σ(I): 2.8 / Redundancy: 7.7 % / Rmerge(I) obs: 0.088 / Rsym value: 0.06 / Net I/σ(I): 11.3
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 2.8 / Num. unique all: 694 / Rsym value: 0.386 / % possible all: 93.2
Reflection
*PLUS
Highest resolution: 3.3 Å / Lowest resolution: 20 Å / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 93.2 % / Rmerge(I) obs: 0.386

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: SIRAS / Resolution: 3.3→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.3253 720 -
Rwork0.2965 --
all-14916 -
obs-14233 95.4 %
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.136 Å28.605 Å20 Å2
2--1.136 Å20 Å2
3----2.272 Å2
Refinement stepCycle: LAST / Resolution: 3.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3403 0 0 0 3403
Xplor fileSerial no: 1 / Param file: protein_rep.param
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONbond_d0.0098
X-RAY DIFFRACTIONangle_d
X-RAY DIFFRACTIONangle_deg2.1

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