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- PDB-5l24: Structure of CNTnw N149L in the intermediate 2 state -

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Basic information

Entry
Database: PDB / ID: 5l24
TitleStructure of CNTnw N149L in the intermediate 2 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.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM100984 United States
Duke University United States
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 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 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
C: Nucleoside permease
B: 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 area8130 Å2
ΔGint-101 kcal/mol
Surface area48770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.160, 116.160, 274.560
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 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (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: 3.93 Å3/Da / Density % sol: 68.7 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 50 mM Mg(OAc)2, 30% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.1→37.5 Å / Num. obs: 16202 / % possible obs: 98.7 % / Redundancy: 11 % / CC1/2: 0.91 / Rpim(I) all: 0.09 / Net I/σ(I): 6.3
Reflection shellResolution: 4.11→4.58 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 2.9 / CC1/2: 0.7 / Rpim(I) all: 0.3 / % possible all: 89.4

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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→36.643 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2985 1141 7.05 %
Rwork0.2705 --
obs0.2725 16180 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.1→36.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8655 0 86 0 8741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018891
X-RAY DIFFRACTIONf_angle_d1.05912104
X-RAY DIFFRACTIONf_dihedral_angle_d8.3212953
X-RAY DIFFRACTIONf_chiral_restr0.0491521
X-RAY DIFFRACTIONf_plane_restr0.0041494
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.1004-4.28670.32541280.32621734X-RAY DIFFRACTION90
4.2867-4.51240.2791480.27141879X-RAY DIFFRACTION100
4.5124-4.79450.31541400.26191915X-RAY DIFFRACTION100
4.7945-5.16380.27991490.26991889X-RAY DIFFRACTION100
5.1638-5.68170.37161360.29911895X-RAY DIFFRACTION100
5.6817-6.49990.3241490.30731923X-RAY DIFFRACTION100
6.4999-8.17410.27861470.24741896X-RAY DIFFRACTION100
8.1741-36.64420.27081440.24061908X-RAY DIFFRACTION99

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