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- PDB-4pd9: Structure of vcCNT-7C8C bound to adenosine -

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Basic information

Entry
Database: PDB / ID: 4pd9
TitleStructure of vcCNT-7C8C bound to adenosine
ComponentsNupC family protein
KeywordsTRANSPORT PROTEIN / membrane protein / sodium-coupled transporter / adenosine / 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
ADENOSINE / Nucleoside permease
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.096 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 / 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_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_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)44,9254
Polymers44,1521
Non-polymers7733
Water543
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)134,77412
Polymers132,4563
Non-polymers2,3189
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 area12020 Å2
ΔGint-147 kcal/mol
Surface area44220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.001, 120.001, 83.488
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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-ADN / ADENOSINE


Mass: 267.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H13N5O4
#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.: 3 / 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: 4.13 Å3/Da / Density % sol: 70.22 %
Crystal growTemperature: 290 K / Method: liquid diffusion / pH: 8.5 / 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: 1.0004 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0004 Å / Relative weight: 1
ReflectionResolution: 3.096→50 Å / Num. obs: 12437 / % possible obs: 99 % / Redundancy: 4.2 % / Biso Wilson estimate: 78.4 Å2 / Rmerge(I) obs: 0.104 / Χ2: 1.038 / Net I/av σ(I): 14.088 / Net I/σ(I): 5.8 / Num. measured all: 52273
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.1-3.153.40.5676030.39696.5
3.15-3.213.80.4886010.42498.4
3.21-3.2740.4296050.46898.7
3.27-3.3440.4066420.50499.7
3.34-3.4140.3536200.50799.4
3.41-3.493.90.3226150.56898.9
3.49-3.584.10.2656170.59799.5
3.58-3.683.90.2436130.75799.2
3.68-3.783.80.2096230.80298.9
3.78-3.913.60.1986021.01997.6
3.91-4.044.30.1676241.0599.2
4.04-4.214.40.1476161.22399.5
4.21-4.44.40.1346321.53799.4
4.4-4.634.40.1236211.70699.4
4.63-4.924.40.1146211.45899.5
4.92-5.34.30.1116261.2998.7
5.3-5.834.90.1076290.99699.8
5.83-6.674.80.0876430.964100
6.67-8.44.60.0536341.16100
8.4-504.80.0576502.38598.2

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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: 3.096→48.723 Å / FOM work R set: 0.7422 / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 32.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2694 625 5.03 %
Rwork0.2242 11804 -
obs0.2258 12429 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 194.84 Å2 / Biso mean: 72.18 Å2 / Biso min: 30.39 Å2
Refinement stepCycle: final / Resolution: 3.096→48.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2925 0 53 3 2981
Biso mean--78.94 54.55 -
Num. residues----404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023047
X-RAY DIFFRACTIONf_angle_d0.6174139
X-RAY DIFFRACTIONf_chiral_restr0.019490
X-RAY DIFFRACTIONf_plane_restr0.003508
X-RAY DIFFRACTIONf_dihedral_angle_d9.8321033
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0964-3.4080.30431470.24992887303497
3.408-3.90090.24311570.21282935309299
3.9009-4.9140.27181580.21629653123100
4.914-48.72910.26911630.22753017318099

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