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- PDB-7dla: Crystal structure of nucleoside transporter NupG (D323A mutant) -

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Basic information

Entry
Database: PDB / ID: 7dla
TitleCrystal structure of nucleoside transporter NupG (D323A mutant)
ComponentsNucleoside permease NupG
KeywordsTRANSPORT PROTEIN / MFS / Nucleoside / Transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


nucleoside:proton symporter activity / cytidine transmembrane transporter activity / uridine transmembrane transport / adenosine transport / nucleoside transmembrane transport / pyrimidine nucleoside transmembrane transporter activity / pyrimidine nucleoside transport / uridine transmembrane transporter activity / purine nucleoside transmembrane transport / plasma membrane
Similarity search - Function
Nucleoside:H+ symporter / Nucleoside permease NupG / Nucleoside H+ symporter / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
Nucleoside permease NupG
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWang, C. / Xiao, Q.J. / Deng, D.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Molecular basis for substrate recognition by the bacterial nucleoside transporter NupG.
Authors: Wang, C. / Xiao, Q. / Duan, H. / Li, J. / Zhang, J. / Wang, Q. / Guo, L. / Hu, J. / Sun, B. / Deng, D.
History
DepositionNov 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoside permease NupG


Theoretical massNumber of molelcules
Total (without water)46,3731
Polymers46,3731
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area17060 Å2
Unit cell
Length a, b, c (Å)145.332, 47.096, 63.383
Angle α, β, γ (deg.)90.000, 94.900, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Nucleoside permease NupG / Nucleoside-transport system protein NupG


Mass: 46372.895 Da / Num. of mol.: 1 / Mutation: D323A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: nupG, b2964, JW2932 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AFF4

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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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.1 M NaCl, 0.1 M MgCl2, 0.1M MES pH6.0, 30% PEG550MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3→19.77 Å / Num. obs: 8747 / % possible obs: 99.6 % / Redundancy: 5.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.173 / Rpim(I) all: 0.081 / Rrim(I) all: 0.191 / Net I/σ(I): 7.5 / Num. measured all: 47341
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3-3.185.60.983790814090.8230.4441.0821.799.9
9-19.774.80.06315183180.9940.0320.07123.890.7

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Predict model from robetta webiste

Resolution: 3→19.766 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2769 869 9.97 %
Rwork0.2339 7848 -
obs0.2382 8717 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.14 Å2 / Biso mean: 64.9623 Å2 / Biso min: 48.13 Å2
Refinement stepCycle: final / Resolution: 3→19.766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3120 0 0 0 3120
Num. residues----402
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0001-3.18730.32871410.29081290100
3.1873-3.43220.35171440.33661303100
3.4322-3.77550.31181410.25491293100
3.7755-4.31680.27591460.2292129599
4.3168-5.42010.26371490.22551311100
5.4201-19.7660.23541480.18581356100

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