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- PDB-8q2o: Structure of alginate transporter AlgE from P. aeruginosa PAO1 by... -

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Basic information

Entry
Database: PDB / ID: 8q2o
TitleStructure of alginate transporter AlgE from P. aeruginosa PAO1 by using Se-MAG for the the lipid cubic phase crystallization
ComponentsAlginate production protein AlgE
KeywordsTRANSPORT PROTEIN / alginate transporter / co-crystallization / experimental phasing / seleno-monoacylglyceride / X-ray scattering
Function / homologyAlginate export domain / : / Alginate export / alginic acid biosynthetic process / cell outer membrane / CITRATE ANION / : / Alginate production protein AlgE
Function and homology information
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsHuang, C.-Y. / Boland, C. / Kaki, S.S. / Wang, M. / Olieric, V. / Caffrey, M.
Funding supportEuropean Union, Ireland, 2items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission701647European Union
Science Foundation Ireland16/IA/4435 Ireland
CitationJournal: Crystals / Year: 2023
Title: Se-MAG Is a Convenient Additive for Experimental Phasing and Structure Determination of Membrane Proteins Crystallised by the Lipid Cubic Phase (In Meso) Method
Authors: Boland, C. / Huang, C.Y. / Shanker Kaki, S. / Wang, M. / Olieric, V. / Caffrey, M.
History
DepositionAug 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alginate production protein AlgE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,41528
Polymers53,5021
Non-polymers7,91327
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.090, 74.490, 115.780
Angle α, β, γ (deg.)90.000, 102.500, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alginate production protein AlgE


Mass: 53502.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: algE, alg76, PA3544 / Production host: Escherichia coli (E. coli) / References: UniProt: P18895

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Non-polymers , 7 types, 341 molecules

#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400


Mass: 398.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#5: Chemical
ChemComp-IRY / [(2~{S})-2,3-bis(oxidanyl)propyl] 8-hexylselanyloctanoate


Mass: 381.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C17H34O4Se / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.25 Å3/Da / Density % sol: 45.24 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 5.6
Details: 41 %(v/v) PEG400, 100 mM LiSO4, and 0.1 M sodium citrate at pH 5.6
PH range: 5.6-6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97794 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97794 Å / Relative weight: 1
ReflectionResolution: 1.7→44.63 Å / Num. obs: 102477 / % possible obs: 100 % / Redundancy: 45.88 % / Biso Wilson estimate: 21.87 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.21 / Net I/σ(I): 17.63
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 9.73 % / Mean I/σ(I) obs: 1.61 / Num. unique obs: 7616 / CC1/2: 0.66 / Rrim(I) all: 1.64 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
XDSVERSION Feb 5, 2021 BUILT=20210323data reduction
XSCALEVERSION Feb 5, 2021 BUILT=20210323data scaling
SHELXCDVersion 2016/1phasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→44.63 Å / SU ML: 0.2135 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.6501
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1992 2606 5 %
Rwork0.1629 49499 -
obs0.1648 52105 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.13 Å2
Refinement stepCycle: LAST / Resolution: 1.7→44.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3635 0 423 315 4373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01444286
X-RAY DIFFRACTIONf_angle_d1.66055687
X-RAY DIFFRACTIONf_chiral_restr0.0998550
X-RAY DIFFRACTIONf_plane_restr0.0145721
X-RAY DIFFRACTIONf_dihedral_angle_d30.20061697
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.730.31081380.26522618X-RAY DIFFRACTION100
1.73-1.760.31471340.23782554X-RAY DIFFRACTION100
1.76-1.80.25721380.2082618X-RAY DIFFRACTION99.89
1.8-1.840.22971350.18122562X-RAY DIFFRACTION99.96
1.84-1.880.19191380.15542619X-RAY DIFFRACTION99.96
1.88-1.930.18421350.14162568X-RAY DIFFRACTION100
1.93-1.980.22141370.14722596X-RAY DIFFRACTION99.89
1.98-2.040.19211380.15422630X-RAY DIFFRACTION100
2.04-2.110.22141350.15392572X-RAY DIFFRACTION100
2.11-2.180.1871370.15262600X-RAY DIFFRACTION100
2.18-2.270.1931370.152591X-RAY DIFFRACTION100
2.27-2.370.2251370.15372602X-RAY DIFFRACTION100
2.37-2.50.20581370.16282610X-RAY DIFFRACTION100
2.5-2.650.22961370.15952603X-RAY DIFFRACTION100
2.65-2.860.19231370.16232607X-RAY DIFFRACTION100
2.86-3.140.19791380.16132624X-RAY DIFFRACTION100
3.14-3.60.1661390.14462632X-RAY DIFFRACTION100
3.6-4.530.18481370.14792604X-RAY DIFFRACTION100
4.54-44.630.19351420.19252689X-RAY DIFFRACTION99.89

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