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- PDB-4rp9: Bacterial vitamin C transporter UlaA/SgaT in C2 form -

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Basic information

Entry
Database: PDB / ID: 4rp9
TitleBacterial vitamin C transporter UlaA/SgaT in C2 form
ComponentsAscorbate-specific permease IIC component UlaA
KeywordsMEMBRANE PROTEIN / PTS / Vitamin C transporter / L-Ascorbate / L-Ascorbate-6-P
Function / homology
Function and homology information


L-ascorbic acid transmembrane transport / protein-phosphocysteine-L-ascorbate-phosphotransferase system transporter activity / transmembrane transporter complex / phosphoenolpyruvate-dependent sugar phosphotransferase system / membrane / identical protein binding / plasma membrane
Similarity search - Function
Phosphotransferase system, sugar-specific permease component / PTS system sugar-specific permease component
Similarity search - Domain/homology
ASCORBIC ACID / TRISTEAROYLGLYCEROL / Ascorbate-specific PTS system EIIC component
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.651 Å
AuthorsWang, J.W.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Crystal structure of a phosphorylation-coupled vitamin C transporter
Authors: Luo, P. / Yu, X. / Wang, W. / Fan, S. / Li, X. / Wang, J.
History
DepositionOct 29, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Structure summary
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ascorbate-specific permease IIC component UlaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4689
Polymers50,7661
Non-polymers2,7028
Water6,684371
1
A: Ascorbate-specific permease IIC component UlaA
hetero molecules

A: Ascorbate-specific permease IIC component UlaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,93618
Polymers101,5322
Non-polymers5,40316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area13750 Å2
ΔGint-33 kcal/mol
Surface area31750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.663, 85.812, 83.236
Angle α, β, γ (deg.)90.00, 127.97, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-624-

HOH

21A-879-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ascorbate-specific permease IIC component UlaA / Ascorbate-specific PTS system EIIC component


Mass: 50766.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: ulaA, sgaT, yjfS, b4193, JW5744 / Production host: Escherichia coli (E. coli) / References: UniProt: P39301

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Sugars , 2 types, 4 molecules

#2: Sugar ChemComp-ASC / ASCORBIC ACID / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O6
#3: Sugar ChemComp-BNG / nonyl beta-D-glucopyranoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 375 molecules

#4: Chemical ChemComp-TGL / TRISTEAROYLGLYCEROL / TRIACYLGLYCEROL / Stearin


Mass: 891.480 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C57H110O6
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 3.15 Å3/Da / Density % sol: 60.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES pH 6.5, 0.1M NaCl, 30%(v/v) polyethyleneglycol(PEG)400, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.02245 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02245 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 71471 / % possible obs: 94.7 %

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.651→32.791 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 16.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.174 3483 4.87 %
Rwork0.1338 --
obs0.1358 71470 94.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.651→32.791 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3450 0 186 371 4007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113741
X-RAY DIFFRACTIONf_angle_d1.3865044
X-RAY DIFFRACTIONf_dihedral_angle_d13.8031366
X-RAY DIFFRACTIONf_chiral_restr0.05589
X-RAY DIFFRACTIONf_plane_restr0.007591
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.651-1.67340.33711020.2517184164
1.6734-1.69730.2791210.2409203272
1.6973-1.72270.2831130.2058235783
1.7227-1.74960.28181330.193274595
1.7496-1.77830.23331300.1768282397
1.7783-1.80890.19911210.1642280498
1.8089-1.84180.2291420.1574276998
1.8418-1.87720.22451350.1464285298
1.8772-1.91550.24381360.1426281098
1.9155-1.95720.19731120.1332283798
1.9572-2.00270.16731320.1262279998
2.0027-2.05280.17171670.1168280998
2.0528-2.10830.1751570.1082280798
2.1083-2.17030.1371530.0998282698
2.1703-2.24030.141480.094279598
2.2403-2.32040.14551560.0962284699
2.3204-2.41330.13341490.0934277898
2.4133-2.52310.15461450.0905286899
2.5231-2.6560.13411480.0968283199
2.656-2.82240.14331570.1038282699
2.8224-3.04010.13951310.1173285598
3.0401-3.34580.17981510.1344276996
3.3458-3.82930.17741460.1394276396
3.8293-4.82210.15861470.1505276795
4.8221-32.79710.20411510.187277894

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