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- PDB-2y5y: Crystal structure of LacY in complex with an affinity inactivator -

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Basic information

Entry
Database: PDB / ID: 2y5y
TitleCrystal structure of LacY in complex with an affinity inactivator
ComponentsLACTOSE PERMEASE
KeywordsTRANSPORT PROTEIN / AFFINITY INACTIVATION
Function / homology
Function and homology information


lactose:proton symporter activity / lactose transport / cytidine transmembrane transporter activity / carbohydrate:proton symporter activity / uridine transmembrane transporter 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 / 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
: / 2-sulfanylethyl beta-D-galactopyranoside / Lactose permease
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.38 Å
AuthorsChaptal, V. / Kwon, S. / Sawaya, M.R. / Guan, L. / Kaback, H.R. / Abramson, J.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Crystal Structure of Lactose Permease in Complex with an Affinity Inactivator Yields Unique Insight Into Sugar Recognition.
Authors: Chaptal, V. / Kwon, S. / Sawaya, M.R. / Guan, L. / Kaback, H.R. / Abramson, J.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: Probing the Mechanism of a Membrane Transport Protein with Affinity Inactivators.
Authors: Guan, L. / Sahin-Toth, M. / Kalai, T. / Hideg, K. / Kaback, H.R.
History
DepositionJan 19, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 30, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2986
Polymers94,5432
Non-polymers7554
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-24.2 kcal/mol
Surface area35720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.560, 127.840, 189.870
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 / LACTOSE-PROTON SYMPORT


Mass: 47271.484 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: METHANE-THIO-SULFONIDE-GALACTOSIDE LINKED BY S-S BOND TO C122.
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K-12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / References: UniProt: P02920
#2: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ba
#3: Sugar ChemComp-TGA / 2-sulfanylethyl beta-D-galactopyranoside / METHANETHIOSULFONYL-GALACTOSIDE / 2-sulfanylethyl beta-D-galactoside / 2-sulfanylethyl D-galactoside / 2-sulfanylethyl galactoside


Type: D-saccharide / Mass: 240.274 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16O6S
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 117 TO SER ENGINEERED RESIDUE IN CHAIN A, ALA 122 TO CYS ...ENGINEERED RESIDUE IN CHAIN A, CYS 117 TO SER ENGINEERED RESIDUE IN CHAIN A, ALA 122 TO CYS ENGINEERED RESIDUE IN CHAIN A, CYS 148 TO ALA ENGINEERED RESIDUE IN CHAIN A, CYS 154 TO VAL ENGINEERED RESIDUE IN CHAIN A, CYS 176 TO MET ENGINEERED RESIDUE IN CHAIN A, CYS 234 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 333 TO SER ENGINEERED RESIDUE IN CHAIN A, CYS 353 TO ALA ENGINEERED RESIDUE IN CHAIN A, CYS 355 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 117 TO SER ENGINEERED RESIDUE IN CHAIN B, ALA 122 TO CYS ENGINEERED RESIDUE IN CHAIN B, CYS 148 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 154 TO VAL ENGINEERED RESIDUE IN CHAIN B, CYS 176 TO MET ENGINEERED RESIDUE IN CHAIN B, CYS 234 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 333 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 353 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 355 TO ALA

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 7.16 Å3/Da / Density % sol: 82.69 %
Description: THE DATA DISPLAYED STRONG ANISOTROPY. THE NON- CORRECTED DATA WAS DEPOSITED IN THE PDB, WHILE THE CORRECTED DATA WAS INITIALLY USED TO SOLVE THE STRUCTURE, WITH BETTER DATA STATISTICS IN ...Description: THE DATA DISPLAYED STRONG ANISOTROPY. THE NON- CORRECTED DATA WAS DEPOSITED IN THE PDB, WHILE THE CORRECTED DATA WAS INITIALLY USED TO SOLVE THE STRUCTURE, WITH BETTER DATA STATISTICS IN THE HIGH RESOLUTION SHELLS.
Crystal growpH: 6 / Details: PH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.4→28.28 Å / Num. obs: 35055 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 45.31 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 4.8
Reflection shellResolution: 3.4→3.5 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.3 / % possible all: 94.3

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PV7

1pv7


Resolution: 3.38→28.28 Å / Cor.coef. Fo:Fc: 0.8747 / Cor.coef. Fo:Fc free: 0.8565 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.3027 1759 5.02 %RANDOM
Rwork0.2864 ---
obs0.2872 35055 --
Displacement parametersBiso mean: 163.55 Å2
Baniso -1Baniso -2Baniso -3
1--9.8398 Å20 Å20 Å2
2---6.5899 Å20 Å2
3---16.4297 Å2
Refine analyzeLuzzati coordinate error obs: 1.298 Å
Refinement stepCycle: LAST / Resolution: 3.38→28.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6177 0 32 0 6209
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0096399HARMONIC2
X-RAY DIFFRACTIONt_angle_deg18661HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2147SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes79HARMONIC2
X-RAY DIFFRACTIONt_gen_planes952HARMONIC5
X-RAY DIFFRACTIONt_it6369HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.04
X-RAY DIFFRACTIONt_other_torsion22.15
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion813SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7546SEMIHARMONIC4
LS refinement shellResolution: 3.38→3.48 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2843 127 5 %
Rwork0.2822 2413 -
all0.2823 2540 -
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1245-1.5090.40564.3839-0.42788.33080.0804-0.0379-0.00690.3248-0.0957-0.09570.38820.31070.01530.3659-0.1511-0.01640.32240.0039-0.241331.1006111.162165.211
20-1.38230.37373.4507-0.76728.32160.00070.2643-0.08370.2322-0.07180.2314-0.1328-0.54050.07110.3664-0.1270.0720.1761-0.0469-0.24259.32369.185167.608
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN B AND (RESID 4:801)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 4:701)

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