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- PDB-4rng: Crystal structure of a bacterial homologue of SWEET transporters -

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Basic information

Entry
Database: PDB / ID: 4rng
TitleCrystal structure of a bacterial homologue of SWEET transporters
ComponentsMtN3/saliva family
KeywordsSUGAR BINDING PROTEIN / SemiSWEET / MtN3 / Sugar Transporter
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
Monooxygenase - #290 / Repeated motif present between transmembrane helices in cystinosin, yeast ERS1p, mannose-P-dolichol utilization defect 1, and other hypothetical proteins. / PQ-loop repeat / PQ loop repeat / Monooxygenase / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / MtN3/saliva family
Similarity search - Component
Biological speciesThermodesulfovibrio yellowstonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsHu, Q. / Wang, J. / Yan, C. / Yan, N.
CitationJournal: Cell Res. / Year: 2014
Title: Crystal structure of a bacterial homologue of SWEET transporters.
Authors: Wang, J. / Yan, C. / Li, Y. / Hirata, K. / Yamamoto, M. / Yan, N. / Hu, Q.
History
DepositionOct 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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: MtN3/saliva family
B: MtN3/saliva family
C: MtN3/saliva family
D: MtN3/saliva family
E: MtN3/saliva family
F: MtN3/saliva family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,23817
Polymers64,1406
Non-polymers2,09911
Water0
1
A: MtN3/saliva family
C: MtN3/saliva family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0256
Polymers21,3802
Non-polymers6454
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-65 kcal/mol
Surface area8580 Å2
MethodPISA
2
B: MtN3/saliva family
D: MtN3/saliva family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6685
Polymers21,3802
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-79 kcal/mol
Surface area8360 Å2
MethodPISA
3
E: MtN3/saliva family
F: MtN3/saliva family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5466
Polymers21,3802
Non-polymers1,1664
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-61 kcal/mol
Surface area8720 Å2
MethodPISA
4
A: MtN3/saliva family
C: MtN3/saliva family
hetero molecules

B: MtN3/saliva family
D: MtN3/saliva family
E: MtN3/saliva family
F: MtN3/saliva family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,23817
Polymers64,1406
Non-polymers2,09911
Water0
TypeNameSymmetry operationNumber
crystal symmetry operation3_445-x-1,y-1/2,-z+1/21
identity operation1_555x,y,z1
Buried area16030 Å2
ΔGint-256 kcal/mol
Surface area21410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.880, 96.155, 119.797
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
MtN3/saliva family


Mass: 10689.952 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermodesulfovibrio yellowstonii (bacteria)
Strain: ATCC 51303 / DSM 11347 / YP87 / Gene: THEYE_A1538 / Production host: Escherichia coli (E. coli) / References: UniProt: B5YGD6
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


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


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4

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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: 2.37 Å3/Da / Density % sol: 48.19 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.2
Details: 2% 3/4 EO/OH (Pentaerythritol ethoxylate), 0.1M Lithium sulphate, 0.1M Sodium citrate pH 5.2, Lipidic cubic phase, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 18, 2014
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. all: 25032 / Num. obs: 23655 / % possible obs: 94.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.4→2.49 Å / % possible all: 95.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4QNC

4qnc


Resolution: 2.4→40 Å / SU ML: 0.31 / σ(F): 1 / Phase error: 33.27 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2936 1123 4.77 %RANDOM
Rwork0.2509 ---
all-25032 --
obs-23655 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3872 0 135 0 4007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014068
X-RAY DIFFRACTIONf_angle_d1.3125480
X-RAY DIFFRACTIONf_dihedral_angle_d14.6641476
X-RAY DIFFRACTIONf_chiral_restr0.06688
X-RAY DIFFRACTIONf_plane_restr0.007616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3864-2.51210.2431680.20961266X-RAY DIFFRACTION38
2.5121-2.66940.28941160.21152441X-RAY DIFFRACTION73
2.6694-2.87530.27841850.2313209X-RAY DIFFRACTION97
2.8753-3.16430.29951600.23733377X-RAY DIFFRACTION100
3.1643-3.62140.26731660.24693200X-RAY DIFFRACTION98
3.6214-4.55950.30511260.23912565X-RAY DIFFRACTION77
4.5595-28.26210.26711600.23893521X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -17.3563 Å / Origin y: -98.8653 Å / Origin z: 30.9782 Å
111213212223313233
T0.213 Å2-0.0099 Å2-0.1128 Å2-0.188 Å2-0.0247 Å2--0.1683 Å2
L0.8883 °20.0436 °20.0186 °2-1.1104 °20.0479 °2--0.111 °2
S0.0129 Å °-0.0404 Å °0.0022 Å °0.0042 Å °-0.0219 Å °-0.0032 Å °0.0643 Å °-0.0175 Å °-0.0211 Å °
Refinement TLS groupSelection details: all

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