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- PDB-5u9w: Structure of CNTnw N149L in the intermediate 3 state -

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Basic information

Entry
Database: PDB / ID: 5u9w
TitleStructure of CNTnw N149L in the intermediate 3 state
ComponentsNucleoside permease
KeywordsTRANSPORT PROTEIN / transporter / nucleoside / elevator-type alternate access
Function / homology
Function and homology information


nucleoside transmembrane transporter activity / symporter activity / plasma membrane
Similarity search - Function
Concentrative nucleoside transporter N-terminal domain / Concentrative nucleoside transporter / Concentrative nucleoside transporter C-terminal domain / Concentrative nucleoside transporter, metazoan/bacterial / Na+ dependent nucleoside transporter N-terminus / Na+ dependent nucleoside transporter C-terminus / Nucleoside transporter/FeoB GTPase, Gate domain / Nucleoside recognition
Similarity search - Domain/homology
Chem-6ZL / Nucleoside permease
Similarity search - Component
Biological speciesNeisseria wadsworthii 9715 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.555 Å
AuthorsHirschi, M. / Johnson, Z.L. / Lee, S.-Y.
CitationJournal: Nature / Year: 2017
Title: Visualizing multistep elevator-like transitions of a nucleoside transporter.
Authors: Hirschi, M. / Johnson, Z.L. / Lee, S.Y.
History
DepositionDec 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2May 17, 2017Group: Database references
Revision 1.3Oct 4, 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: Nucleoside permease
B: Nucleoside permease
C: Nucleoside permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,9195
Polymers134,0213
Non-polymers1,8982
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-101 kcal/mol
Surface area47840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.588, 115.588, 272.394
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Nucleoside permease


Mass: 44673.602 Da / Num. of mol.: 3 / Mutation: N149L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria wadsworthii 9715 (bacteria) / Gene: nupC, HMPREF9370_1765 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: G4CRQ5
#2: Chemical ChemComp-6ZL / 2-{[(4-O-alpha-D-glucopyranosyl-beta-D-glucopyranosyl)oxy]methyl}-2-octyldecyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside


Mass: 949.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C43H80O22

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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: 3.66 Å3/Da / Density % sol: 66.4 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 10mM Mg(OAc)2, 25% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97779 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97779 Å / Relative weight: 1
ReflectionResolution: 3.55→30 Å / Num. obs: 24655 / % possible obs: 99.9 % / Redundancy: 8.4 % / CC1/2: 0.93 / Rpim(I) all: 0.05 / Net I/σ(I): 16.4
Reflection shellResolution: 3.55→3.61 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 1.7 / CC1/2: 0.56 / Rpim(I) all: 0.69 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000v705adata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L26

5l26


Resolution: 3.555→29.964 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.8
RfactorNum. reflection% reflection
Rfree0.2756 3463 7.1 %
Rwork0.2531 --
obs0.2547 24655 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.555→29.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8616 0 53 0 8669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018818
X-RAY DIFFRACTIONf_angle_d0.97412023
X-RAY DIFFRACTIONf_dihedral_angle_d7.6152885
X-RAY DIFFRACTIONf_chiral_restr0.0461515
X-RAY DIFFRACTIONf_plane_restr0.0041495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5546-3.60320.40221450.39191760X-RAY DIFFRACTION97
3.6032-3.65460.38051280.341812X-RAY DIFFRACTION100
3.6546-3.70910.35131520.32771779X-RAY DIFFRACTION100
3.7091-3.76690.33281500.31431821X-RAY DIFFRACTION100
3.7669-3.82860.28321500.28731810X-RAY DIFFRACTION100
3.8286-3.89450.29631090.30281839X-RAY DIFFRACTION100
3.8945-3.96510.27021440.28111824X-RAY DIFFRACTION100
3.9651-4.04120.31681280.27951797X-RAY DIFFRACTION100
4.0412-4.12350.3141400.27821868X-RAY DIFFRACTION100
4.1235-4.21290.23521380.27791786X-RAY DIFFRACTION100
4.2129-4.31060.26291440.25761822X-RAY DIFFRACTION100
4.3106-4.41810.25251340.25031811X-RAY DIFFRACTION100
4.4181-4.53720.25271460.23981815X-RAY DIFFRACTION100
4.5372-4.67020.25131420.25571801X-RAY DIFFRACTION100
4.6702-4.82040.24491300.24531858X-RAY DIFFRACTION100
4.8204-4.99190.2441420.25331824X-RAY DIFFRACTION100
4.9919-5.19080.25741240.26551833X-RAY DIFFRACTION100
5.1908-5.42570.32521400.26981784X-RAY DIFFRACTION100
5.4257-5.70990.33851330.2851827X-RAY DIFFRACTION100
5.7099-6.06490.36411540.2741830X-RAY DIFFRACTION100
6.0649-6.52870.31171320.27711786X-RAY DIFFRACTION100
6.5287-7.17750.28711480.24631834X-RAY DIFFRACTION100
7.1775-8.19740.23491320.20621823X-RAY DIFFRACTION100
8.1974-10.25860.18331340.16481813X-RAY DIFFRACTION100
10.2586-29.96480.28691440.26841774X-RAY DIFFRACTION98

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