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- PDB-4pd6: Crystal structure of vcCNT-7C8C bound to uridine -

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Basic information

Entry
Database: PDB / ID: 4pd6
TitleCrystal structure of vcCNT-7C8C bound to uridine
ComponentsNupC family protein
KeywordsTRANSPORT PROTEIN / membrane protein / sodium-coupled transporter / drug transporter / uridine
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
URIDINE / Nucleoside permease
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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 17, 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 / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_audit_support / pdbx_database_related / 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_related.content_type / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification
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

Downloads & links

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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
Water2,342130
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 area11790 Å2
ΔGint-95 kcal/mol
Surface area41910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.650, 119.650, 83.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Detailsbiological unit is the same as asym.

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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-URI / URIDINE


Mass: 244.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N2O6
#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.: 130 / 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: 4.09 Å3/Da / Density % sol: 69.91 %
Crystal growTemperature: 290 K / Method: liquid diffusion / pH: 9.5 / 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: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 40394 / % possible obs: 99.3 % / Redundancy: 5.9 % / Biso Wilson estimate: 41.34 Å2 / Rmerge(I) obs: 0.052 / Χ2: 1.622 / Net I/av σ(I): 42 / Net I/σ(I): 15.3 / Num. measured all: 238922
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.08-2.124.30.55418370.89191.8
2.12-2.154.90.52420040.90998.2
2.15-2.25.30.46520010.9299.2
2.2-2.245.50.40420171.0599.8
2.24-2.295.60.31520061.29699.7
2.29-2.345.80.26620201.06999.9
2.34-2.45.90.21220241.09999.9
2.4-2.4760.18320391.187100
2.47-2.546.10.15220151.241100
2.54-2.626.20.13920121.342100
2.62-2.716.20.11220311.537100
2.71-2.826.30.09820321.672100
2.82-2.956.30.08520271.781100
2.95-3.116.40.07220421.922100
3.11-3.36.40.0620462.076100
3.3-3.566.30.05420262.392100
3.56-3.915.90.05120362.945100
3.91-4.486.30.04120372.726100
4.48-5.646.30.03320632.03100
5.64-506.10.02520791.48998.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.4_1496)refinement
SCALEPACKdata scaling
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TIJ

3tij


Resolution: 2.08→35.43 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.233 2063 5.11 %
Rwork0.202 --
obs0.204 40368 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.72 Å2
Refinement stepCycle: final / Resolution: 2.08→35.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2834 0 53 130 3017
Biso mean--52.92 54.43 -
Num. residues----401
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052945
X-RAY DIFFRACTIONf_angle_d0.7823997
X-RAY DIFFRACTIONf_dihedral_angle_d12.088999
X-RAY DIFFRACTIONf_chiral_restr0.029481
X-RAY DIFFRACTIONf_plane_restr0.003498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0814-2.12980.29861250.2832381X-RAY DIFFRACTION93
2.1298-2.1830.29751510.26662507X-RAY DIFFRACTION99
2.183-2.24210.30881300.26752561X-RAY DIFFRACTION100
2.2421-2.3080.29441440.27182558X-RAY DIFFRACTION100
2.308-2.38250.24971400.22122553X-RAY DIFFRACTION100
2.3825-2.46760.24111420.20252545X-RAY DIFFRACTION100
2.4676-2.56640.22551300.18792554X-RAY DIFFRACTION100
2.5664-2.68320.21421380.18572570X-RAY DIFFRACTION100
2.6832-2.82460.19861330.18342563X-RAY DIFFRACTION100
2.8246-3.00150.21181420.19332572X-RAY DIFFRACTION100
3.0015-3.23310.19441370.1932580X-RAY DIFFRACTION100
3.2331-3.55810.22021350.18952574X-RAY DIFFRACTION100
3.5581-4.07240.21861380.192576X-RAY DIFFRACTION100
4.0724-5.12830.22051370.19652591X-RAY DIFFRACTION100
5.1283-35.43310.26621410.20892620X-RAY DIFFRACTION99

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