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- PDB-4qnd: Crystal structure of a SemiSWEET -

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Basic information

Entry
Database: PDB / ID: 4qnd
TitleCrystal structure of a SemiSWEET
ComponentsChemical transport protein
KeywordsMEMBRANE PROTEIN / transporter
Function / homology
Function and homology information


identical protein binding / membrane / plasma membrane
Similarity search - Function
Monooxygenase - #290 / Monooxygenase / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PENTADECANE / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Sugar transporter SemiSWEET
Similarity search - Component
Biological speciesVibrio sp. N418 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.698 Å
AuthorsYan, X. / Yuyong, T. / Liang, F. / Perry, K.
CitationJournal: Nature / Year: 2014
Title: Structures of bacterial homologues of SWEET transporters in two distinct conformations.
Authors: Xu, Y. / Tao, Y. / Cheung, L.S. / Fan, C. / Chen, L.Q. / Xu, S. / Perry, K. / Frommer, W.B. / Feng, L.
History
DepositionJun 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2014Group: Database references
Revision 1.2Dec 17, 2014Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Chemical transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0157
Polymers11,1221
Non-polymers1,8936
Water1,17165
1
A: Chemical transport protein
hetero molecules

A: Chemical transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,03014
Polymers22,2452
Non-polymers3,78612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area6290 Å2
ΔGint-16 kcal/mol
Surface area10870 Å2
MethodPISA
2
A: Chemical transport protein
hetero molecules

A: Chemical transport protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,03014
Polymers22,2452
Non-polymers3,78612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x+1/2,y,-z+3/41
Buried area3230 Å2
ΔGint-26 kcal/mol
Surface area13940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.236, 58.236, 172.923
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-224-

HOH

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Components

#1: Protein Chemical transport protein


Mass: 11122.296 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio sp. N418 (bacteria) / Gene: VIBRN418_06191 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F9RBV9
#2: Chemical ChemComp-MYS / PENTADECANE


Mass: 212.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H32
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400


Mass: 398.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 3.3 Å3/Da / Density % sol: 62.68 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.5
Details: 50mM Mes pH6.5, 100mM MgCl2, 30% PEG400, lipid cubic phase, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 18, 2013
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.698→55.19 Å / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 15
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2 % / Rmerge(I) obs: 0.883 / Mean I/σ(I) obs: 0.8 / Rsym value: 88.3 / % possible all: 76.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.698→55.19 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 22.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.206 1547 9.98 %
Rwork0.1982 --
obs0.199 15505 91.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.698→55.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms760 0 117 65 942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003893
X-RAY DIFFRACTIONf_angle_d0.8111178
X-RAY DIFFRACTIONf_dihedral_angle_d18.041362
X-RAY DIFFRACTIONf_chiral_restr0.029130
X-RAY DIFFRACTIONf_plane_restr0.004123
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.698-1.75280.4442930.357843X-RAY DIFFRACTION61
1.7528-1.81550.30761140.30821065X-RAY DIFFRACTION78
1.8155-1.88820.25981310.24921203X-RAY DIFFRACTION88
1.8882-1.97410.2511340.21391242X-RAY DIFFRACTION91
1.9741-2.07820.25241430.19051267X-RAY DIFFRACTION93
2.0782-2.20840.20331480.16721321X-RAY DIFFRACTION96
2.2084-2.37890.16341520.16771343X-RAY DIFFRACTION98
2.3789-2.61830.22171530.17061369X-RAY DIFFRACTION99
2.6183-2.99710.1711530.1731385X-RAY DIFFRACTION99
2.9971-3.7760.19481580.17581415X-RAY DIFFRACTION100
3.776-55.21940.19181680.2221505X-RAY DIFFRACTION99

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