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- PDB-5l27: Structure of CNTnw N149L in the intermediate 1 state -

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Basic information

Entry
Database: PDB / ID: 5l27
TitleStructure of CNTnw N149L in the intermediate 1 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: 4.1 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 1.3Oct 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)134,9704
Polymers134,0213
Non-polymers9491
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7570 Å2
ΔGint-99 kcal/mol
Surface area50620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.100, 116.100, 272.180
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.: 1 / 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: 4.12 Å3/Da / Density % sol: 70.18 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 50 mM Mg(OAc)2, 30% PEG400, 100 mM KCl, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Oct 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.1→37.64 Å / Num. obs: 16224 / % possible obs: 99.9 % / Redundancy: 4.7 % / CC1/2: 0.98 / Rpim(I) all: 0.06 / Net I/σ(I): 7.3
Reflection shellResolution: 4.1→4.58 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 2.4 / CC1/2: 0.69 / Rpim(I) all: 0.48 / % possible all: 99.9

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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: 4.1→37.638 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3086 1141 7.04 %
Rwork0.2687 --
obs0.2716 16208 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.1→37.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8288 0 53 0 8341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038484
X-RAY DIFFRACTIONf_angle_d0.7111589
X-RAY DIFFRACTIONf_dihedral_angle_d8.5372706
X-RAY DIFFRACTIONf_chiral_restr0.0311471
X-RAY DIFFRACTIONf_plane_restr0.0031444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.1002-4.28650.37751380.31391885X-RAY DIFFRACTION100
4.2865-4.51220.31911430.27831869X-RAY DIFFRACTION100
4.5122-4.79440.28411430.26691885X-RAY DIFFRACTION100
4.7944-5.16370.28021440.25841883X-RAY DIFFRACTION100
5.1637-5.68170.36121430.28451894X-RAY DIFFRACTION100
5.6817-6.50030.37321430.29281889X-RAY DIFFRACTION100
6.5003-8.17580.28781450.26541883X-RAY DIFFRACTION100
8.1758-37.63910.27791420.24521879X-RAY DIFFRACTION98

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