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- PDB-4pb1: Structure of vcCNT-7C8C bound to ribavirin -

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Basic information

Entry
Database: PDB / ID: 4pb1
TitleStructure of vcCNT-7C8C bound to ribavirin
ComponentsNupC family protein
KeywordsTRANSPORT PROTEIN / membrane protein / sodium-coupled transporter / ribavirin / drug transporter
Function / homology
Function and homology information


nucleoside transmembrane transport / nucleoside transmembrane transporter activity / symporter activity / identical protein binding / 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-RBV / Nucleoside permease
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.803 Å
AuthorsJohnson, Z.L. / Lee, S.-Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM100984 United States
CitationJournal: Elife / Year: 2014
Title: Structural basis of nucleoside and nucleoside drug selectivity by concentrative nucleoside transporters.
Authors: Johnson, Z.L. / Lee, J.H. / Lee, K. / Lee, M. / Kwon, D.Y. / Hong, J. / Lee, S.Y.
History
DepositionApr 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / software
Item: _entity.pdbx_description / _entity.src_method ..._entity.pdbx_description / _entity.src_method / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NupC family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9024
Polymers44,1521
Non-polymers7503
Water362
1
A: NupC family protein
hetero molecules

A: NupC family protein
hetero molecules

A: NupC family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,70512
Polymers132,4563
Non-polymers2,2499
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area10370 Å2
ΔGint-151 kcal/mol
Surface area45150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.749, 119.749, 83.638
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein NupC family protein


Mass: 44151.848 Da / Num. of mol.: 1 / Mutation: L7C, I8C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_2352 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: Q9KPL5
#2: Chemical ChemComp-RBV / 1-(beta-D-ribofuranosyl)-1H-1,2,4-triazole-3-carboxamide / Ribavirin


Mass: 244.205 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12N4O5
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: 70.14 %
Crystal growTemperature: 290 K / Method: liquid diffusion / pH: 7.5 / Details: 37-42% PEG 400, 100 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 16852 / % possible obs: 99.8 % / Redundancy: 7 % / Biso Wilson estimate: 62.17 Å2 / Rmerge(I) obs: 0.114 / Χ2: 2.588 / Net I/av σ(I): 20.172 / Net I/σ(I): 8.3 / Num. measured all: 117518
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.8-2.856.30.7588230.564100
2.85-2.96.50.688400.59299.9
2.9-2.966.60.6248310.60599.8
2.96-3.026.60.558380.6599.9
3.02-3.086.60.4678430.659100
3.08-3.156.70.4198330.692100
3.15-3.236.90.328480.765100
3.23-3.326.90.2838400.80199.9
3.32-3.426.90.2358320.87100
3.42-3.5370.2098391.195100
3.53-3.657.10.1548491.06699.9
3.65-3.87.20.168331.724100
3.8-3.977.20.1438502.289100
3.97-4.187.30.088381.19599.8
4.18-4.447.40.0678481.32499.9
4.44-4.797.40.068461.62699.9
4.79-5.277.30.0658452.36599.8
5.27-6.037.30.0738552.3299.8
6.03-7.597.10.0568515.1399.6
7.59-507.20.07887023.14798.5

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TIJ

3tij


Resolution: 2.803→39.197 Å / FOM work R set: 0.8042 / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2589 853 5.07 %
Rwork0.2221 15987 -
obs0.2238 16840 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.17 Å2 / Biso mean: 58.84 Å2 / Biso min: 25.95 Å2
Refinement stepCycle: final / Resolution: 2.803→39.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2947 0 51 2 3000
Biso mean--66.11 48.1 -
Num. residues----404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033066
X-RAY DIFFRACTIONf_angle_d0.7094159
X-RAY DIFFRACTIONf_chiral_restr0.023490
X-RAY DIFFRACTIONf_plane_restr0.003512
X-RAY DIFFRACTIONf_dihedral_angle_d11.0081052
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8028-2.97840.2981430.25726352778100
2.9784-3.20820.26021360.239226552791100
3.2082-3.53090.22811390.209126412780100
3.5309-4.04140.24281440.201926732817100
4.0414-5.090.24471440.213626692813100
5.09-39.20090.28131470.23382714286199

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