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- PDB-1pv6: Crystal structure of lactose permease -

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Basic information

Entry
Database: PDB / ID: 1pv6
TitleCrystal structure of lactose permease
ComponentsLactose permease
KeywordsTRANSPORT PROTEIN / Transport / Sugar transport / Symport / membrane protein
Function / homology
Function and homology information


lactose:proton symporter activity / lactose transport / carbohydrate:proton symporter activity / lactose binding / carbohydrate transport / membrane / plasma membrane
Similarity search - Function
LacY/RafB permease family / LacY/RafB permease family, conserved site / LacY proton/sugar symporter / LacY family proton/sugar symporters signature 1. / LacY family proton/sugar symporters signature 2. / MFS general substrate transporter like domains / Growth Hormone; Chain: A; / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily ...LacY/RafB permease family / LacY/RafB permease family, conserved site / LacY proton/sugar symporter / LacY family proton/sugar symporters signature 1. / LacY family proton/sugar symporters signature 2. / MFS general substrate transporter like domains / 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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.5 Å
AuthorsAbramson, J. / Smirnova, I. / Kasho, V. / Verner, G. / Kaback, H.R. / Iwata, S.
CitationJournal: SCIENCE / Year: 2003
Title: Structure and mechanism of the lactose permease of Escherichia coli
Authors: Abramson, J. / Smirnova, I. / Kasho, V. / Verner, G. / Kaback, H.R. / Iwata, S.
History
DepositionJun 26, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 12, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lactose permease
B: Lactose permease


Theoretical massNumber of molelcules
Total (without water)92,9702
Polymers92,9702
Non-polymers00
Water00
1
A: Lactose permease


Theoretical massNumber of molelcules
Total (without water)46,4851
Polymers46,4851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lactose permease


Theoretical massNumber of molelcules
Total (without water)46,4851
Polymers46,4851
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.351, 125.845, 188.118
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lactose permease


Mass: 46484.797 Da / Num. of mol.: 2 / Mutation: C154G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P02920

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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: 6.45 Å3/Da
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMHEPES1reservoirpH7.0
227-30 %PEG4001reservoir
3200 mM1reservoirCaCl2
43 %1,6-hexanediol1reservoir
50.8 mMCHAPS1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.009 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 28, 2003
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 3.5→40 Å / Num. all: 31004 / Num. obs: 25733 / % possible obs: 83 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1
Reflection shellResolution: 3.5→3.6 Å / % possible all: 71.8
Reflection
*PLUS
Num. obs: 25917 / % possible obs: 85.9 % / Redundancy: 2.9 % / Num. measured all: 63863 / Rmerge(I) obs: 0.075
Reflection shell
*PLUS
% possible obs: 71.8 % / Rmerge(I) obs: 0.461

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 3.5→40 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.337 1310 random
Rwork0.294 --
obs0.294 25733 -
all-31004 -
Refinement stepCycle: LAST / Resolution: 3.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6580 0 0 0 6580
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d19.6
X-RAY DIFFRACTIONc_improper_angle_d1
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1
LS refinement shell
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 3.6 Å / Rfactor Rfree: 0.379 / Rfactor Rwork: 0.356

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