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- PDB-2v8n: Wild-type Structure of Lactose Permease -

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Basic information

Entry
Database: PDB / ID: 2v8n
TitleWild-type Structure of Lactose Permease
ComponentsLACTOSE PERMEASE
KeywordsTRANSPORT PROTEIN / TRANSMEMBRANE / INNER MEMBRANE / SUGAR TRANSPORT / SYMPORT / MEMBRANE / TRANSPORT / FORMYLATION
Function / homology
Function and homology information


lactose:proton symporter activity / lactose transport / carbohydrate:proton symporter activity / lactose binding / organic substance transport / 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 / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / Growth Hormone; Chain: A; / 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 / 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
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsGuan, L. / Mirza, O. / Verner, G. / Iwata, S. / Kaback, H.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Structural Determination of Wild-Type Lactose Permease.
Authors: Guan, L. / Mirza, O. / Verner, G. / Iwata, S. / Kaback, H.R.
History
DepositionAug 9, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LACTOSE PERMEASE
B: LACTOSE PERMEASE


Theoretical massNumber of molelcules
Total (without water)93,0622
Polymers93,0622
Non-polymers00
Water0
1
A: LACTOSE PERMEASE


Theoretical massNumber of molelcules
Total (without water)46,5311
Polymers46,5311
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: LACTOSE PERMEASE


Theoretical massNumber of molelcules
Total (without water)46,5311
Polymers46,5311
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)101.370, 127.400, 188.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.004175, 1, -5.2E-5), (0.9997, 0.004175, 0.02503), (0.02503, 5.2E-5, -0.9997)
Vector: -52.03, 33.7, 329.1)

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Components

#1: Protein LACTOSE PERMEASE / / LACTOSE-PROTON SYMPORT


Mass: 46530.891 Da / Num. of mol.: 2
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: 6.54 Å3/Da / Description: NONE
Crystal growpH: 8 / Details: pH 8.0

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→40 Å / Num. obs: 24578 / % possible obs: 85.8 % / Observed criterion σ(I): 0.5 / Redundancy: 2.5 % / Rmerge(I) obs: 0.12
Reflection shellResolution: 3.6→3.73 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.49 / % possible all: 75.6

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PV7

1pv7


Resolution: 3.6→10 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 2463788.54 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.333 1117 4.9 %RANDOM
Rwork0.294 ---
obs0.294 22746 82.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.6158 Å2 / ksol: 0.220414 e/Å3
Displacement parametersBiso mean: 85.3 Å2
Baniso -1Baniso -2Baniso -3
1-20.91 Å20 Å20 Å2
2--11.12 Å20 Å2
3----32.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.74 Å0.61 Å
Luzzati d res low-5 Å
Luzzati sigma a1.44 Å1.23 Å
Refinement stepCycle: LAST / Resolution: 3.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6584 0 0 0 6584
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0
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
LS refinement shellResolution: 3.6→3.81 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.416 163 4.9 %
Rwork0.392 3175 -
obs--73.8 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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