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- PDB-7dl9: Crystal structure of nucleoside transporter NupG -

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Basic information

Entry
Database: PDB / ID: 7dl9
TitleCrystal structure of nucleoside transporter NupG
ComponentsNucleoside permease NupG
KeywordsTRANSPORT PROTEIN / MFS / Nucleoside / Transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


nucleoside:proton symporter activity / uridine transmembrane transport / adenosine transport / cytidine transmembrane transporter activity / pyrimidine nucleoside transmembrane transporter activity / uridine transmembrane transporter activity / pyrimidine nucleoside transport / purine nucleoside transmembrane transport / : / plasma membrane => GO:0005886 / plasma membrane
Similarity search - Function
Nucleoside:H+ symporter / Nucleoside permease NupG / Nucleoside H+ symporter / Major facilitator superfamily domain / Major facilitator superfamily (MFS) profile. / MFS transporter superfamily
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Nucleoside permease NupG
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWang, C. / Xiao, Q.J. / Deng, D.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Molecular basis for substrate recognition by the bacterial nucleoside transporter NupG.
Authors: Wang, C. / Xiao, Q. / Duan, H. / Li, J. / Zhang, J. / Wang, Q. / Guo, L. / Hu, J. / Sun, B. / Deng, D.
History
DepositionNov 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoside permease NupG
B: Nucleoside permease NupG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,5474
Polymers92,8342
Non-polymers7132
Water30617
1
A: Nucleoside permease NupG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1303
Polymers46,4171
Non-polymers7132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nucleoside permease NupG


Theoretical massNumber of molelcules
Total (without water)46,4171
Polymers46,4171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.874, 68.715, 79.027
Angle α, β, γ (deg.)81.110, 74.270, 84.020
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 92 or resid 94...
21(chain B and (resid 1 through 62 or (resid 63...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETPROPRO(chain A and (resid 1 through 92 or resid 94...AA1 - 921 - 92
12ALAALAASNASN(chain A and (resid 1 through 92 or resid 94...AA94 - 20794 - 207
13METMETLYSLYS(chain A and (resid 1 through 92 or resid 94...AA1 - 4051 - 405
14METMETLYSLYS(chain A and (resid 1 through 92 or resid 94...AA1 - 4051 - 405
15PHEPHEGLNGLN(chain A and (resid 1 through 92 or resid 94...AA244 - 251244 - 251
16ALAALAALAALA(chain A and (resid 1 through 92 or resid 94...AA253 - 340253 - 340
17ILEILEILEILE(chain A and (resid 1 through 92 or resid 94...AA341341
18METMETLYSLYS(chain A and (resid 1 through 92 or resid 94...AA1 - 4051 - 405
19METMETLYSLYS(chain A and (resid 1 through 92 or resid 94...AA1 - 4051 - 405
110METMETLYSLYS(chain A and (resid 1 through 92 or resid 94...AA1 - 4051 - 405
111METMETLYSLYS(chain A and (resid 1 through 92 or resid 94...AA1 - 4051 - 405
21METMETALAALA(chain B and (resid 1 through 62 or (resid 63...BB1 - 621 - 62
22ASPASPASPASP(chain B and (resid 1 through 62 or (resid 63...BB6363
23METMETLYSLYS(chain B and (resid 1 through 62 or (resid 63...BB1 - 4051 - 405
24METMETLYSLYS(chain B and (resid 1 through 62 or (resid 63...BB1 - 4051 - 405
25METMETLYSLYS(chain B and (resid 1 through 62 or (resid 63...BB1 - 4051 - 405
26METMETLYSLYS(chain B and (resid 1 through 62 or (resid 63...BB1 - 4051 - 405

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Components

#1: Protein Nucleoside permease NupG / Nucleoside-transport system protein NupG


Mass: 46416.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: nupG, b2964, JW2932 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AFF4
#2: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.1 M Citrate sodium (pH=5), 0.1 M NaCl 0.1 M MgCl2 , 30% PEG 600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3→29.54 Å / Num. obs: 16931 / % possible obs: 98.8 % / Redundancy: 3.5 % / CC1/2: 0.986 / Rmerge(I) obs: 0.153 / Net I/σ(I): 6.8 / Num. measured all: 59909
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
3-3.183.60.452991427270.8922.898.5
9-29.543.40.05820776170.99514.195.7

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: predicted model by the robetta website

Resolution: 3→25.566 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 28.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2798 1691 10.01 %
Rwork0.2504 15200 -
obs0.2534 16891 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.16 Å2 / Biso mean: 29.3306 Å2 / Biso min: 1.59 Å2
Refinement stepCycle: final / Resolution: 3→25.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6295 0 30 17 6342
Biso mean--26.49 24.14 -
Num. residues----810
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3469X-RAY DIFFRACTION12.704TORSIONAL
12B3469X-RAY DIFFRACTION12.704TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0001-3.08830.26991410.2208126999
3.0883-3.18780.30641390.2404124898
3.1878-3.30150.28971460.2504130598
3.3015-3.43340.28641400.2412125999
3.4334-3.58920.28291390.2399126199
3.5892-3.77790.29931380.2238123999
3.7779-4.01380.25231420.2518128199
4.0138-4.32230.27861410.2478127999
4.3223-4.75480.27471430.2618127098
4.7548-5.4370.27981390.2729125799
5.437-6.82840.30961410.2828126499
6.8284-25.5660.25641420.2497126899

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