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- PDB-4x5n: Crystal structure of SemiSWEET in the inward-open and outward-ope... -

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Basic information

Entry
Database: PDB / ID: 4x5n
TitleCrystal structure of SemiSWEET in the inward-open and outward-open conformations
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
Sugar transporter SemiSWEET / Sugar transporter SemiSWEET
Similarity search - Component
Biological speciesEscherichia coli UMEA 3162-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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 1.3Nov 8, 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
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
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)44,9334
Polymers44,9334
Non-polymers00
Water00
1
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)22,4672
Polymers22,4672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-33 kcal/mol
Surface area10160 Å2
MethodPISA
2
C: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)22,4672
Polymers22,4672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-34 kcal/mol
Surface area9810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.010, 34.630, 123.220
Angle α, β, γ (deg.)90.00, 102.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Uncharacterized protein


Mass: 11233.304 Da / Num. of mol.: 4
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.96 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 8
Details: 23% PEG550MME, 100mM Tris-HCl (pH 8.0), 350mM NH4-citrate, 3% dimethyl sulfoxide

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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: Dec 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 9943 / % possible obs: 98 % / Redundancy: 3.3 % / Net I/σ(I): 8.2
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 1.7 / % possible all: 98.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.3_1479) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X5M

4x5m


Resolution: 3→47.135 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3281 779 7.84 %
Rwork0.281 --
obs0.2847 9936 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→47.135 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2679 0 0 0 2679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032733
X-RAY DIFFRACTIONf_angle_d0.7123743
X-RAY DIFFRACTIONf_dihedral_angle_d14.551867
X-RAY DIFFRACTIONf_chiral_restr0.025495
X-RAY DIFFRACTIONf_plane_restr0.005445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0002-3.18810.32831280.2821498X-RAY DIFFRACTION98
3.1881-3.43420.4151310.31791540X-RAY DIFFRACTION99
3.4342-3.77960.33541260.29541493X-RAY DIFFRACTION98
3.7796-4.32620.3111310.27051531X-RAY DIFFRACTION98
4.3262-5.44930.36621260.28251489X-RAY DIFFRACTION96
5.4493-47.14070.28141370.26741606X-RAY DIFFRACTION98

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