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- PDB-3tij: Crystal structure of a concentrative nucleoside transporter from ... -

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Basic information

Entry
Database: PDB / ID: 3tij
TitleCrystal structure of a concentrative nucleoside transporter from Vibrio cholerae
ComponentsNupC family protein
KeywordsMEMBRANE PROTEIN / membrane transporter / nucleoside transporter / drug transporter / uridine / nucleosides
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.436 Å
AuthorsJohnson, Z.L. / Cheong, C.-G. / Lee, S.-Y.
CitationJournal: Nature / Year: 2012
Title: Crystal structure of a concentrative nucleoside transporter from Vibrio cholerae at 2.4A
Authors: Johnson, Z.L. / Cheong, C.G. / Lee, S.Y.
History
DepositionAug 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)46,8528
Polymers44,1721
Non-polymers2,6807
Water77543
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)140,55624
Polymers132,5163
Non-polymers8,04021
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 area16310 Å2
ΔGint-87 kcal/mol
Surface area44530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.717, 119.717, 83.136
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein NupC family protein


Mass: 44171.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: VC_2352 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: Q9KPL5
#2: Chemical ChemComp-URI / URIDINE


Mass: 244.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N2O6
#3: Sugar
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 3.89 Å3/Da / Density % sol: 68.41 %
Crystal growTemperature: 290 K / Method: microbatch-under-oil / pH: 9
Details: 100 mM CaCl2, 40% PEG400, 100 mM Tris pH 9.0, microbatch-under-oil, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1.06223 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 14, 2011
RadiationMonochromator: Rosenbaum-Rock monochromator high-resolution double-crystal Si (111) sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06223 Å / Relative weight: 1
ReflectionResolution: 2.42→50 Å / Num. all: 49041 / Num. obs: 49037 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 7.9 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 28.256
Reflection shellResolution: 2.42→2.46 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1213 / % possible all: 98.3

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.436→28.755 Å / SU ML: 0.64 / σ(F): 1.38 / Phase error: 21.83 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2278 2472 5.04 %RANDOM
Rwork0.196 ---
obs0.1975 49037 98.47 %-
all-49041 --
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.23 Å2 / ksol: 0.337 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.5719 Å2-0 Å20 Å2
2---2.5719 Å2-0 Å2
3---5.1437 Å2
Refinement stepCycle: LAST / Resolution: 2.436→28.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2951 0 76 43 3070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073091
X-RAY DIFFRACTIONf_angle_d0.9374182
X-RAY DIFFRACTIONf_dihedral_angle_d13.3741067
X-RAY DIFFRACTIONf_chiral_restr0.061492
X-RAY DIFFRACTIONf_plane_restr0.003511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4363-2.48310.31381310.27552400X-RAY DIFFRACTION93
2.4831-2.53380.30571260.26072597X-RAY DIFFRACTION97
2.5338-2.58890.26381300.2422535X-RAY DIFFRACTION97
2.5889-2.6490.28071420.23872587X-RAY DIFFRACTION98
2.649-2.71520.2721370.21092551X-RAY DIFFRACTION98
2.7152-2.78860.1961350.21172597X-RAY DIFFRACTION98
2.7886-2.87060.24561400.19882584X-RAY DIFFRACTION99
2.8706-2.96310.23761420.20412589X-RAY DIFFRACTION99
2.9631-3.06890.2431390.21132596X-RAY DIFFRACTION99
3.0689-3.19170.25061320.19612621X-RAY DIFFRACTION99
3.1917-3.33670.1891410.19242608X-RAY DIFFRACTION99
3.3367-3.51230.22051420.1792610X-RAY DIFFRACTION99
3.5123-3.7320.23071400.17562643X-RAY DIFFRACTION100
3.732-4.01940.19951310.18062601X-RAY DIFFRACTION99
4.0194-4.42260.23861440.17262618X-RAY DIFFRACTION100
4.4226-5.05950.23891390.17762603X-RAY DIFFRACTION100
5.0595-6.36310.21921400.22022642X-RAY DIFFRACTION100
6.3631-28.75710.20351410.19932583X-RAY DIFFRACTION98

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