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- PDB-4x5m: Crystal structure of SemiSWEET in the inward-open conformation -

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Basic information

Entry
Database: PDB / ID: 4x5m
TitleCrystal structure of SemiSWEET in the inward-open conformation
ComponentsUncharacterized protein
KeywordsTRANSPORT PROTEIN / SWEET / PQLC / membrane protein / sugar transporter
Function / homology
Function and homology information


sugar transmembrane transporter activity / carbohydrate transport / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Monooxygenase - #290 / : / PQ-loop repeat / PQ loop repeat / Monooxygenase / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
OLEIC ACID / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Sugar transporter SemiSWEET / Sugar transporter SemiSWEET
Similarity search - Component
Biological speciesEscherichia coli UMEA 3162-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsLee, Y. / Nishizawa, T. / Yamashita, K. / Ishitani, R. / Nureki, O.
CitationJournal: Nat Commun / Year: 2015
Title: Structural basis for the facilitative diffusion mechanism by SemiSWEET transporter
Authors: Lee, Y. / Nishizawa, T. / Yamashita, K. / Ishitani, R. / Nureki, O.
History
DepositionDec 5, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Derived calculations / Source and taxonomy
Category: diffrn_source / entity_src_gen / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,42520
Polymers33,7003
Non-polymers4,72517
Water1,18966
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,87410
Polymers22,4672
Non-polymers2,4088
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
Buried area4040 Å2
ΔGint-41 kcal/mol
Surface area11340 Å2
MethodPISA
2
B: Uncharacterized protein
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,98815
Polymers22,4672
Non-polymers3,52113
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6770 Å2
ΔGint-58 kcal/mol
Surface area11040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.680, 102.120, 58.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Uncharacterized protein


Mass: 11233.304 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli UMEA 3162-1 (bacteria)
Gene: G925_04926 / Production host: Escherichia coli (E. coli) / References: UniProt: T8UDF6, UniProt: P0DMV3*PLUS

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Non-polymers , 5 types, 83 molecules

#2: Chemical
ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C18H34O2
#3: Chemical ChemComp-OLB / (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.69 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8
Details: 28% PEG550MME, 100 mM Tris-HCl (pH 8.0), 350 mM MgSO4, 3% galactose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 22575 / % possible obs: 99.9 % / Redundancy: 19.53 % / Net I/σ(I): 17.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 18.01 % / Rmerge(I) obs: 0.01809 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2→47.515 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2238 2260 10.02 %
Rwork0.1965 --
obs0.1992 22564 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→47.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2077 0 259 66 2402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022360
X-RAY DIFFRACTIONf_angle_d0.6393133
X-RAY DIFFRACTIONf_dihedral_angle_d16.314898
X-RAY DIFFRACTIONf_chiral_restr0.021381
X-RAY DIFFRACTIONf_plane_restr0.004360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.04350.33861370.27391251X-RAY DIFFRACTION100
2.0435-2.09110.25841390.26031253X-RAY DIFFRACTION100
2.0911-2.14340.27081370.22221248X-RAY DIFFRACTION100
2.1434-2.20130.22611390.21011235X-RAY DIFFRACTION100
2.2013-2.26610.25771410.20721259X-RAY DIFFRACTION100
2.2661-2.33920.25871370.20761247X-RAY DIFFRACTION100
2.3392-2.42290.25061550.20631232X-RAY DIFFRACTION100
2.4229-2.51990.21211370.19141249X-RAY DIFFRACTION100
2.5199-2.63450.1991350.18821255X-RAY DIFFRACTION100
2.6345-2.77340.23421380.19451266X-RAY DIFFRACTION100
2.7734-2.94720.25511400.19921293X-RAY DIFFRACTION100
2.9472-3.17470.21951390.20691267X-RAY DIFFRACTION100
3.1747-3.4940.19891450.20011272X-RAY DIFFRACTION100
3.494-3.99940.1931420.18111288X-RAY DIFFRACTION100
3.9994-5.0380.19961490.16541303X-RAY DIFFRACTION100
5.038-47.52870.2471500.20711386X-RAY DIFFRACTION100

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