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- PDB-4oaa: Crystal structure of E. coli lactose permease G46W,G262W bound to... -

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Basic information

Entry
Database: PDB / ID: 4oaa
TitleCrystal structure of E. coli lactose permease G46W,G262W bound to sugar
ComponentsLactose/galactose transporter
KeywordsTRANSPORT PROTEIN / transmembrane helices helix bundles / sugar transport / symport / major facilitator superfamily / D-galactose D-galactopyranosides
Function / homologyMFS general substrate transporter like domains / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha / thiodigalactoside / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsKumar, H. / Kasho, V. / Smirnova, I. / Finer-Moore, J. / Kaback, H.R. / Stroud, R.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure of sugar-bound LacY.
Authors: Kumar, H. / Kasho, V. / Smirnova, I. / Finer-Moore, J.S. / Kaback, H.R. / Stroud, R.M.
History
DepositionJan 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity.src_method / _entity.type / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Aug 12, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / pdbx_branch_scheme / pdbx_entity_branch_descriptor / pdbx_molecule_features / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _chem_comp.pdbx_synonyms / _pdbx_branch_scheme.pdb_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr2_auth_asym_id
Revision 3.1Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lactose/galactose transporter
B: Lactose/galactose transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2954
Polymers93,5782
Non-polymers7172
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-20 kcal/mol
Surface area34040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.560, 121.940, 264.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Lactose/galactose transporter


Mass: 46789.207 Da / Num. of mol.: 2 / Mutation: G46W, G262W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: lacY, ECDH10B_1356 / Plasmid: pT7-5 / Production host: Escherichia coli (E. coli) / Strain (production host): C21 / References: UniProt: B1XBJ1
#2: Polysaccharide beta-D-galactopyranose-(1-1)-1-thio-beta-D-galactopyranose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 358.362 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with S-glycosidic bond between monosaccharides, and with reducing-end-to-reducing-end glycosidic bond
References: thiodigalactoside
DescriptorTypeProgram
[][b-D-Galp1SH]{[(1+S)][b-D-Galp]{}}LINUCSPDB-CARE

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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: 4.37 Å3/Da / Density % sol: 71.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10mg/ml protein (20mM Hepes, .2% NG)and 5mM TDG against 1M NaCl, 0.05M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2013 / Details: monochrometer
RadiationMonochromator: double flat, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 2.98→44 Å / Num. all: 32186 / Num. obs: 31737 / % possible obs: 95.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 167 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.47
Reflection shellResolution: 2.98→3.2 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 0.08 / % possible all: 61.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
PHASERphasing
ELVESrefinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CFQ

2cfq


Resolution: 3.5→44 Å / SU ML: 0.84 / Isotropic thermal model: isotropic / σ(F): 1.34 / Phase error: 39.49 / Stereochemistry target values: ML
Details: hydrogens in riding positions, TLS refinement in final cycles (single group) Ramachandran restraints for final cycle
RfactorNum. reflection% reflection
Rfree0.2929 1077 5.14 %
Rwork0.2565 --
obs0.2583 20954 99.38 %
all-20954 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6211 0 46 0 6257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066451
X-RAY DIFFRACTIONf_angle_d0.8998750
X-RAY DIFFRACTIONf_dihedral_angle_d14.4182170
X-RAY DIFFRACTIONf_chiral_restr0.048995
X-RAY DIFFRACTIONf_plane_restr0.0041054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.65920.4631430.42952442X-RAY DIFFRACTION100
3.6592-3.8520.38951250.38092437X-RAY DIFFRACTION100
3.852-4.09320.36551480.33892472X-RAY DIFFRACTION100
4.0932-4.4090.34141330.29282490X-RAY DIFFRACTION100
4.409-4.85220.33171270.23982480X-RAY DIFFRACTION100
4.8522-5.55310.3291410.25182484X-RAY DIFFRACTION100
5.5531-6.99180.36391300.27822519X-RAY DIFFRACTION100
6.9918-44.00510.21531300.21612553X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 19.7872 Å / Origin y: -31.7937 Å / Origin z: 33.4496 Å
111213212223313233
T1.0696 Å20.0092 Å20.1478 Å2-1.0445 Å20.0596 Å2--1.1187 Å2
L2.0633 °20.9792 °21.7654 °2-1.6818 °21.4145 °2--2.7408 °2
S-0.0735 Å °-0.082 Å °0.1345 Å °0.2288 Å °-0.0338 Å °0.2375 Å °-0.0983 Å °-0.3249 Å °0.1005 Å °
Refinement TLS groupSelection details: all

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