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- PDB-4zyr: Crystal structure of E. coli Lactose permease G46W/G262W bound to... -

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Basic information

Entry
Database: PDB / ID: 4zyr
TitleCrystal structure of E. coli Lactose permease G46W/G262W bound to p-nitrophenyl alpha-D-galactopyranoside (alpha-NPG)
ComponentsLactose permease
KeywordsTRANSPORT PROTEIN / Membrane Protein / Transporter / Alpha-Helical / Major Facilitator Superfamily (MFS)
Function / homology
Function and homology information


lactose:proton symporter activity / lactose transport / cytidine transmembrane transporter activity / lactose binding / carbohydrate:proton symporter activity / uridine transmembrane transporter activity / : / 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
4-nitrophenyl alpha-D-galactopyranoside / Lactose permease
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.312 Å
AuthorsKumar, H. / Finer-Moore, J.S. / Kaback, H.R. / Stroud, R.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37GM024485 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK069463 United States
National Science Foundation (NSF, United States)MCB-1129551 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structure of LacY with an alpha-substituted galactoside: Connecting the binding site to the protonation site.
Authors: Kumar, H. / Finer-Moore, J.S. / Kaback, H.R. / Stroud, R.M.
History
DepositionMay 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Aug 12, 2015Group: Derived calculations
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)94,7946
Polymers93,5782
Non-polymers1,2154
Water0
1
A: Lactose permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3973
Polymers46,7891
Non-polymers6082
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lactose permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3973
Polymers46,7891
Non-polymers6082
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.150, 121.990, 266.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 6 - 408 / Label seq-ID: 6 - 408

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Lactose permease / / Lactose-proton symport


Mass: 46789.207 Da / Num. of mol.: 2 / Mutation: G46W, G262W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: lacY, b0343, JW0334 / Plasmid: pT7-5 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): C41 / References: UniProt: P02920
#2: Sugar ChemComp-9PG / 4-nitrophenyl alpha-D-galactopyranoside / 4-nitrophenyl alpha-D-galactoside / 4-nitrophenyl D-galactoside / 4-nitrophenyl galactoside


Type: D-saccharide / Mass: 301.249 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15NO8
#3: Sugar ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.81 Å3/Da / Density % sol: 74.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.0 M NaCl 0.05 M Tris (pH8.0) 26% PEG 600

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 17, 2015
RadiationMonochromator: double flat Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionHighest resolution: 3.3 Å / Num. obs: 25009 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 125.69 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.148 / Rrim(I) all: 0.167 / Χ2: 1.006 / Net I/σ(I): 10.5 / Num. measured all: 114039
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
3.3-3.50.1234.060.5217863407639583.93997.1
3.5-3.80.4521.641.1621472468946471.8499.1
3.8-40.6131.1451.9510748235823301.29298.8
4-50.9360.3156.6231855700468780.35798.2
5-60.9750.16210.7213865311130180.18497
6-80.9960.06421.2610844253324260.07395.8
8-1010.01657.9936489088530.01993.9
10-1510.01276.8927326946480.01493.4
15-2010.00987.036801781630.0191.6
20-3010.0190.3430193770.01282.8
300.9990.01374.383147110.01723.4

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Processing

Software
NameVersionClassification
PHENIXdev_1700refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OAA

4oaa


Resolution: 3.312→37.036 Å / SU ML: 0.63 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2779 1954 8.01 %
Rwork0.2586 22440 -
obs0.2602 24394 96.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 314.35 Å2 / Biso mean: 141.791 Å2 / Biso min: 16.07 Å2
Refinement stepCycle: final / Resolution: 3.312→37.036 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6157 0 114 0 6271
Biso mean--108.18 --
Num. residues----772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046435
X-RAY DIFFRACTIONf_angle_d0.8538717
X-RAY DIFFRACTIONf_chiral_restr0.036981
X-RAY DIFFRACTIONf_plane_restr0.0051049
X-RAY DIFFRACTIONf_dihedral_angle_d14.3012163
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3297X-RAY DIFFRACTION12.46TORSIONAL
12B3297X-RAY DIFFRACTION12.46TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.3119-3.39470.40411200.4071355147584
3.3947-3.48640.41111420.39631593173596
3.4864-3.58890.40551380.38741595173398
3.5889-3.70460.48091400.41221595173596
3.7046-3.83690.34641420.34121624176699
3.8369-3.99030.34671420.32591644178699
3.9903-4.17170.30131400.30771628176899
4.1717-4.39130.32241400.27221618175898
4.3913-4.6660.27671430.24491639178298
4.666-5.02540.22491410.21741633177498
5.0254-5.52970.27311410.24221622176397
5.5297-6.32640.30071400.25321617175797
6.3264-7.95750.25081440.23581652179696
7.9575-37.03860.21331410.20561625176692

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