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- PDB-4rp8: Bacterial vitamin C transporter UlaA/SgaT in P21 form -

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Basic information

Entry
Database: PDB / ID: 4rp8
TitleBacterial vitamin C transporter UlaA/SgaT in P21 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


protein-phosphocysteine-L-ascorbate-phosphotransferase system transporter activity / L-ascorbic acid transmembrane transport / phosphoenolpyruvate-dependent sugar phosphotransferase system / transmembrane transporter complex / 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 / Ascorbate-specific PTS system EIIC component
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.359 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
Revision 1.3Aug 24, 2022Group: Database references / Structure summary / Category: chem_comp / citation / database_2
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: Ascorbate-specific permease IIC component UlaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,1915
Polymers101,5322
Non-polymers6593
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-25 kcal/mol
Surface area32190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.781, 85.561, 88.954
Angle α, β, γ (deg.)90.00, 96.73, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 50766.160 Da / Num. of mol.: 2
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
#2: Sugar ChemComp-ASC / ASCORBIC ACID / Vitamin C / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O6 / Comment: medication*YM
#3: Sugar ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 3.12 Å3/Da / Density % sol: 60.56 %
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: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 49177 / % possible obs: 96.1 %

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RP9

4rp9


Resolution: 2.359→38.503 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 23.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2388 2539 5.17 %
Rwork0.1968 --
obs0.1989 49141 95.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.359→38.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6650 0 45 194 6889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056856
X-RAY DIFFRACTIONf_angle_d0.9459313
X-RAY DIFFRACTIONf_dihedral_angle_d12.4722345
X-RAY DIFFRACTIONf_chiral_restr0.0311103
X-RAY DIFFRACTIONf_plane_restr0.0041120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.359-2.40440.28761450.24852171X-RAY DIFFRACTION80
2.4044-2.45350.29061330.24372562X-RAY DIFFRACTION95
2.4535-2.50680.28151250.22952560X-RAY DIFFRACTION95
2.5068-2.56510.29861410.22512576X-RAY DIFFRACTION95
2.5651-2.62930.27281290.22152593X-RAY DIFFRACTION96
2.6293-2.70030.28851470.20992584X-RAY DIFFRACTION96
2.7003-2.77980.25881400.18882606X-RAY DIFFRACTION96
2.7798-2.86950.24961610.1962614X-RAY DIFFRACTION96
2.8695-2.9720.26331390.18442609X-RAY DIFFRACTION97
2.972-3.09090.22231530.18562618X-RAY DIFFRACTION97
3.0909-3.23150.20931630.18762611X-RAY DIFFRACTION97
3.2315-3.40180.23031670.17442616X-RAY DIFFRACTION97
3.4018-3.61480.20871300.17712642X-RAY DIFFRACTION97
3.6148-3.89370.19861280.17462648X-RAY DIFFRACTION97
3.8937-4.2850.21381260.17782662X-RAY DIFFRACTION97
4.285-4.9040.21321070.19042652X-RAY DIFFRACTION96
4.904-6.17440.24451480.22132583X-RAY DIFFRACTION94
6.1744-38.50840.26231570.21182695X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.05230.0168-0.07590.00870.01990.1735-0.0463-0.1206-0.01090.03090.1053-0.0229-0.0574-0.1220.00940.18940.0097-0.0110.2015-0.03660.1862-27.70578.0417-15.5739
20.2767-0.1646-0.16260.091-0.00340.41940.03560.09350.0742-0.1117-0.0473-0.11970.0092-0.1509-0.00120.08850.0041-0.00420.0632-0.00610.0891-29.82413.09393.0802
30.0537-0.0278-0.02210.03110.02310.04070.0461-0.07910.1625-0.0086-0.03960.0528-0.0573-0.0293-0.02380.3164-0.3828-0.07430.1514-0.02810.4038-2.313821.8584-6.6788
40.2340.0820.13410.07590.04930.094-0.15810.05890.0307-0.1736-0.1408-0.00590.18750.0968-0.07560.19090.06290.06280.29090.00560.14530.1036-0.833-15.0625
50.01390.01160.01030.0474-0.06130.0547-0.0006-0.111-0.0284-0.05590.00660.0352-0.2170.0654-0.00370.20570.03320.02410.191-0.02310.1557-18.808111.7645-15.3289
60.2374-0.0155-0.00580.180.15980.24040.06590.00560.1116-0.15950.0896-0.0558-0.03110.20240.2290.03520.0426-0.01380.15540.05650.0688-15.60342.86883.0468
70.15090.0006-0.0490.1363-0.0670.0259-0.12570.0640.05250.039-0.055-0.0155-0.2595-0.086-0.06270.14670.2272-0.0386-0.1467-0.04850.0656-34.694113.868915.778
8-0.00360.0243-0.02820.0087-0.03470.079-0.01680.036-0.0204-0.10460.0152-0.03120.04640.0890.00430.2017-0.06770.04390.1676-0.02560.1403-4.74418.5083-30.2903
90.25980.10.0154-0.00310.08230.32510.0002-0.24660.1625-0.0327-0.04380.0158-0.1101-0.045-0.06310.088-0.00830.0389-0.19620.1215-0-9.82467.8182-46.608
100.1132-0.15590.08840.2351-0.10670.1838-0.18080.028-0.16470.0453-0.11740.00340.1352-0.0802-0.23430.06330.01280.11930.2775-0.11450.2575-35.46911.0823-30.7384
110.0117-0.0259-0.02370.05260.05940.0277-0.0459-0.00820.0006-0.0668-0.02820.0227-0.2282-0.0859-0.03550.1583-0.06860.02260.1235-0.03990.1102-16.046911.4348-30.4565
120.2356-0.10120.05270.14330.02590.4392-0.0053-0.01830.04480.05280.02170.084-0.0841-0.10880.07170.10640.0002-0.00040.1334-0.00680.1363-17.30296.5043-50.3876
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 15:76 )A15 - 76
2X-RAY DIFFRACTION2( CHAIN A AND RESID 77:209 )A77 - 209
3X-RAY DIFFRACTION3( CHAIN A AND RESID 210:231 )A210 - 231
4X-RAY DIFFRACTION4( CHAIN A AND RESID 232:264 )A232 - 264
5X-RAY DIFFRACTION5( CHAIN A AND RESID 265:304 )A265 - 304
6X-RAY DIFFRACTION6( CHAIN A AND RESID 305:428 )A305 - 428
7X-RAY DIFFRACTION7( CHAIN A AND RESID 429:456 )A429 - 456
8X-RAY DIFFRACTION8( CHAIN C AND RESID 15:85 )C15 - 85
9X-RAY DIFFRACTION9( CHAIN C AND RESID 86:231 )C86 - 231
10X-RAY DIFFRACTION10( CHAIN C AND RESID 232:264 )C232 - 264
11X-RAY DIFFRACTION11( CHAIN C AND RESID 265:304 )C265 - 304
12X-RAY DIFFRACTION12( CHAIN C AND RESID 305:456 )C305 - 456

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