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- PDB-3qe7: Crystal Structure of Uracil Transporter--UraA -

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Basic information

Entry
Database: PDB / ID: 3qe7
TitleCrystal Structure of Uracil Transporter--UraA
ComponentsUracil permease
KeywordsTRANSPORT PROTEIN / Uracil permease / Uracil transporter / UraA / transporter / inner membrane protein
Function / homology
Function and homology information


uracil:monoatomic cation symporter activity / uracil transport / uracil import across plasma membrane / uracil transmembrane transporter activity / protein homodimerization activity / membrane / plasma membrane
Similarity search - Function
Xanthine/uracil permease / Xanthine/uracil permeases family signature. / Nucleobase cation symporter 2 family / Permease family
Similarity search - Domain/homology
URACIL / Uracil permease
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.781 Å
AuthorsLu, F.R. / Li, S. / Yan, N.
CitationJournal: Nature / Year: 2011
Title: Structure and mechanism of the uracil transporter UraA
Authors: Lu, F. / Li, S. / Jiang, Y. / Jiang, J. / Fan, H. / Lu, G. / Deng, D. / Dang, S. / Zhang, X. / Wang, J. / Yan, N.
History
DepositionJan 20, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 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 1.3Mar 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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: Uracil permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5083
Polymers45,0901
Non-polymers4182
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Uracil permease
hetero molecules

A: Uracil permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0176
Polymers90,1802
Non-polymers8374
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/31
Buried area1930 Å2
ΔGint-18 kcal/mol
Surface area36040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.76, 96.76, 251.95
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Uracil permease / Uracil transporter


Mass: 45089.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: uraA, b2497, JW2482 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AGM7
#2: Chemical ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N2O2
#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.: 1
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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.78 Å3/Da / Density % sol: 67.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 400, 100mM MES-NaOH, 300mM Li2SO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.99294 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 12, 2010
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99294 Å / Relative weight: 1
ReflectionResolution: 2.781→41.92 Å / Num. obs: 18225 / % possible obs: 98.7 % / Redundancy: 4.3 % / Biso Wilson estimate: 78.5 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 17.8
Reflection shellResolution: 2.78→2.88 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.783 / Mean I/σ(I) obs: 1.9 / % possible all: 99.1

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Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.3_473)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.781→41.92 Å / FOM work R set: 0.772 / SU ML: 0.46 / σ(F): 1.34 / Phase error: 28.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3035 930 5.11 %Random
Rwork0.2478 ---
obs0.2506 18200 98.96 %-
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.203 Å2 / ksol: 0.303 e/Å3
Displacement parametersBiso mean: 77.2341 Å2
Baniso -1Baniso -2Baniso -3
1-7.3303 Å20 Å2-0 Å2
2--7.3303 Å20 Å2
3----14.6606 Å2
Refinement stepCycle: LAST / Resolution: 2.781→41.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3001 0 29 0 3030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0333282
X-RAY DIFFRACTIONf_angle_d0.9564223
X-RAY DIFFRACTIONf_dihedral_angle_d14.6251085
X-RAY DIFFRACTIONf_chiral_restr0.071538
X-RAY DIFFRACTIONf_plane_restr0.007507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7808-2.92730.35081440.30042395X-RAY DIFFRACTION99
2.9273-3.11070.31671460.2822388X-RAY DIFFRACTION99
3.1107-3.35080.29871280.23612434X-RAY DIFFRACTION100
3.3508-3.68780.26541460.20412419X-RAY DIFFRACTION99
3.6878-4.2210.26621150.21182494X-RAY DIFFRACTION99
4.221-5.31630.28071270.22292507X-RAY DIFFRACTION99
5.3163-41.92460.35541240.29152633X-RAY DIFFRACTION96
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)
11.01522.01290.47890.9584-0.29161.51870.0617-0.1110.06820.26220.1414-0.10610.0507-0.0887-0.06380.15240.18860.05180.48260.13620.340218.8031-8.588733.082
21.65990.3193-1.20592.3628-0.34822.93610.4202-0.67140.02710.19-0.0647-0.1654-0.24750.1575-0.14640.2970.26890.07370.6644-0.02580.223130.6274.903232.6248
30.1760.8003-0.21752.36680.24542.5023-0.11180.03520.2391-0.05090.28540.1061-0.1046-0.3511-0.20420.05450.056-0.03460.46720.14630.216826.53594.036514.8986
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 330:429
2X-RAY DIFFRACTION2chain A and resid 112:209
3X-RAY DIFFRACTION3chain A and (resid 1:111 or resid 210:329)

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