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- PDB-5xls: Crystal structure of UraA in occluded conformation -

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Basic information

Entry
Database: PDB / ID: 5xls
TitleCrystal structure of UraA in occluded conformation
ComponentsUracil permease
KeywordsTRANSPORT PROTEIN / Occluded conformation / dimer
Function / homology
Function and homology information


uracil transmembrane transporter activity / membrane => GO:0016020 / plasma membrane
Similarity search - Function
: / Xanthine/uracil permease / Xanthine/uracil permeases family signature. / Nucleobase cation symporter 2 family / Permease family
Similarity search - Domain/homology
12-TUNGSTOPHOSPHATE / URACIL / Uracil permease
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsYu, X.Z. / Yang, G.H. / Yan, C.Y. / Yan, N.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology of China2015CB910101, 2016YFA0500402, 2014ZX09507003-006 China
National Natural Science Foundation of China China
CitationJournal: Cell Res. / Year: 2017
Title: Dimeric structure of the uracil:proton symporter UraA provides mechanistic insights into the SLC4/23/26 transporters
Authors: Yu, X. / Yang, G. / Yan, C. / Baylon, J.L. / Jiang, J. / Fan, H. / Lu, G. / Hasegawa, K. / Okumura, H. / Wang, T. / Tajkhorshid, E. / Li, S. / Yan, N.
History
DepositionMay 11, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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

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Assembly

Deposited unit
A: Uracil permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8134
Polymers45,9471
Non-polymers5,8663
Water75742
1
A: Uracil permease
hetero molecules

A: Uracil permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,6268
Polymers91,8932
Non-polymers11,7326
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)74.721, 134.726, 143.452
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 Uracil permease / Uracil transporter


Mass: 45946.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: uraA, Z3760, ECs3359 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AGM8
#2: Chemical ChemComp-URA / URACIL / Uracil


Mass: 112.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N2O2
#3: Chemical ChemComp-KEG / 12-TUNGSTOPHOSPHATE


Mass: 2877.030 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O40PW12
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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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: 3.93 Å3/Da / Density % sol: 68.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 24% PEG 400, 100mM MES-NaOH, pH 6.5, 100mM NaF, 50mM MgCl2, 3mM (NH4)2WS4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 49846 / % possible obs: 98 % / Redundancy: 3.3 % / Rsym value: 0.117 / Net I/σ(I): 18.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 2.8 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QE7

3qe7


Resolution: 2.5→32.79 Å / Cross valid method: FREE R-VALUE / σ(F): 0.88
Details: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS AND I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2469 2318 5.12 %
Rwork0.2257 --
obs0.2268 45247 93.02 %
Solvent computationShrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Bsol: 42.511 Å2 / ksol: 0.313 e/Å3
Refinement stepCycle: LAST / Resolution: 2.5→32.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3001 0 112 42 3155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0323224
X-RAY DIFFRACTIONf_angle_d5.8194641
X-RAY DIFFRACTIONf_dihedral_angle_d27.9811165
X-RAY DIFFRACTIONf_chiral_restr0.107545
X-RAY DIFFRACTIONf_plane_restr0.006508
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4955-2.54640.32241300.31972218X-RAY DIFFRACTION82
2.5464-2.60170.3261240.3042480X-RAY DIFFRACTION92
2.6017-2.66220.31121130.2792626X-RAY DIFFRACTION93
2.6622-2.72880.29261000.27122523X-RAY DIFFRACTION93
2.7288-2.80250.30561240.26432546X-RAY DIFFRACTION93
2.8025-2.88490.22551450.2322547X-RAY DIFFRACTION94
2.8849-2.9780.30781810.23552490X-RAY DIFFRACTION93
2.978-3.08430.27551400.22512564X-RAY DIFFRACTION94
3.0843-3.20770.23811430.22612540X-RAY DIFFRACTION94
3.2077-3.35360.25571310.22172561X-RAY DIFFRACTION94
3.3536-3.53020.27051600.22572555X-RAY DIFFRACTION94
3.5302-3.75110.23851430.22322551X-RAY DIFFRACTION95
3.7511-4.04020.21781190.21682604X-RAY DIFFRACTION95
4.0402-4.44590.20791360.19632564X-RAY DIFFRACTION95
4.4459-5.08720.21121590.20122530X-RAY DIFFRACTION93
5.0872-6.40150.24371480.24112533X-RAY DIFFRACTION94
6.4015-32.79260.24051220.20972497X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: 19.2014 Å / Origin y: 15.5427 Å / Origin z: -12.0268 Å
111213212223313233
T0.266 Å2-0.0113 Å2-0.0449 Å2-0.3062 Å20.0284 Å2--0.2691 Å2
L1.3514 °20.3102 °20.1043 °2-2.4625 °2-0.3645 °2--1.809 °2
S-0.1286 Å °0.1587 Å °0.3056 Å °-0.2776 Å °0.1394 Å °0.1665 Å °-0.1521 Å °-0.0726 Å °-0.0229 Å °
Refinement TLS groupSelection details: all

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