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- PDB-5l2b: Structure of CNTnw N149S, E332A in an outward-facing state -

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Basic information

Entry
Database: PDB / ID: 5l2b
TitleStructure of CNTnw N149S, E332A in an outward-facing 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: 3.8 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
DepositionJul 31, 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 10, 2017Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type
Revision 1.4Oct 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)136,6166
Polymers133,7683
Non-polymers2,8473
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8730 Å2
ΔGint-101 kcal/mol
Surface area47060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.040, 121.040, 277.440
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: 44589.488 Da / Num. of mol.: 3 / Mutation: N149S, E322A
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.: 3 / 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: 4.39 Å3/Da / Density % sol: 71.96 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200 mM choline chloride, 14% Poly(ethylene glycol) monomethyl ether 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3.8→98.06 Å / Num. obs: 22489 / % possible obs: 99.4 % / Redundancy: 4.3 % / CC1/2: 0.99 / Rpim(I) all: 0.08 / Net I/σ(I): 6.2
Reflection shellResolution: 3.8→4.1 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2 / CC1/2: 0.54 / Rpim(I) all: 0.54 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLM7.2.1data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L26

5l26


Resolution: 3.8→98.058 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2895 1583 7.04 %
Rwork0.2505 --
obs0.2533 22476 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.8→98.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8682 0 88 0 8770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038930
X-RAY DIFFRACTIONf_angle_d0.72412186
X-RAY DIFFRACTIONf_dihedral_angle_d9.152905
X-RAY DIFFRACTIONf_chiral_restr0.0271542
X-RAY DIFFRACTIONf_plane_restr0.0051504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8001-3.92270.30281440.28331918X-RAY DIFFRACTION100
3.9227-4.0630.29591500.28221874X-RAY DIFFRACTION100
4.063-4.22560.33081380.28191882X-RAY DIFFRACTION98
4.2256-4.41790.29451410.24151899X-RAY DIFFRACTION100
4.4179-4.65090.31181420.22891944X-RAY DIFFRACTION100
4.6509-4.94220.25091490.22711874X-RAY DIFFRACTION100
4.9422-5.32380.27531410.25261887X-RAY DIFFRACTION98
5.3238-5.85950.35691420.26031900X-RAY DIFFRACTION100
5.8595-6.70720.28651460.25611925X-RAY DIFFRACTION100
6.7072-8.44970.24631450.21841888X-RAY DIFFRACTION99
8.4497-98.09070.2861450.25561902X-RAY DIFFRACTION98

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