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- PDB-7acg: In meso structure of the alginate exporter, AlgE, from Pseudomona... -

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Basic information

Entry
Database: PDB / ID: 7acg
TitleIn meso structure of the alginate exporter, AlgE, from Pseudomonas aeruginosa in 9.8 monoacylglycerol
ComponentsAlginate biosynthesis protein AlgE
KeywordsMEMBRANE PROTEIN / Transporter / Barrel
Function / homology
Function and homology information


alginic acid biosynthetic process / cell outer membrane
Similarity search - Function
Porin - #100 / Alginate export domain / : / Alginate export / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Chem-LH9 / Alginate biosynthesis protein AlgE / Alginate production protein AlgE
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSmithers, L. / van Dalsen, L. / Boland, C. / Caffrey, M.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland Ireland
CitationJournal: Cryst.Growth Des. / Year: 2020
Title: 9.8 MAG. A new host lipid for in meso (lipid cubic phase) crystallization of integral membrane proteins
Authors: van Dalsen, L. / Smithers, L. / Boland, C. / Weichert, D. / Caffrey, M.
History
DepositionSep 10, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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: Alginate biosynthesis protein AlgE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,92618
Polymers53,5021
Non-polymers4,42417
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-36 kcal/mol
Surface area21200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.751, 74.187, 114.992
Angle α, β, γ (deg.)90.000, 102.732, 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 biosynthesis protein AlgE / Alginate export family protein / Alginate production outer membrane protein / Alginate production ...Alginate export family protein / Alginate production outer membrane protein / Alginate production protein AlgE / Transcriptional regulator


Mass: 53502.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: algE, CGU42_05540, EQH76_07525, F3H14_18260, FC629_07390, GNQ48_06715, IPC1323_01805, IPC1509_00845, IPC669_06720, NCTC12934_05462, NCTC13437_03064, PaeAG1_01671, PAMH19_1548, RW109_RW109_02276
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A080VSR9, UniProt: P18895*PLUS

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Non-polymers , 8 types, 131 molecules

#2: Chemical
ChemComp-LH9 / [(2~{S})-2,3-bis(oxidanyl)propyl] heptadec-9-enoate


Mass: 342.513 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C20H38O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#7: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.21 Å3/Da / Density % sol: 44.26 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: PEG400, lithium sulphate, ammonium sulphate, sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→44.37 Å / Num. obs: 39482 / % possible obs: 99.08 % / Redundancy: 6.9 % / Biso Wilson estimate: 26.24 Å2 / CC1/2: 0.99 / Net I/σ(I): 8.35
Reflection shellResolution: 1.85→1.916 Å / Mean I/σ(I) obs: 1.36 / Num. unique obs: 3904 / CC1/2: 0.61

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AFK

4afk


Resolution: 1.85→44.37 Å / SU ML: 0.2292 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.4007
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2204 1982 5.03 %
Rwork0.1836 37433 -
obs0.1855 39415 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.46 Å2
Refinement stepCycle: LAST / Resolution: 1.85→44.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3620 0 305 114 4039
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00584043
X-RAY DIFFRACTIONf_angle_d1.0515400
X-RAY DIFFRACTIONf_chiral_restr0.0483526
X-RAY DIFFRACTIONf_plane_restr0.0042696
X-RAY DIFFRACTIONf_dihedral_angle_d24.7093754
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.33861430.28462630X-RAY DIFFRACTION98.89
1.9-1.950.32331370.24982719X-RAY DIFFRACTION99.34
1.95-20.241380.2252611X-RAY DIFFRACTION98.81
2-2.070.24391320.21692644X-RAY DIFFRACTION98.16
2.07-2.140.27931340.19342663X-RAY DIFFRACTION99.54
2.14-2.230.24091200.18762723X-RAY DIFFRACTION99.41
2.23-2.330.26011470.18432676X-RAY DIFFRACTION99.47
2.33-2.450.24981610.18042667X-RAY DIFFRACTION99.47
2.45-2.610.24211370.18222686X-RAY DIFFRACTION99.51
2.61-2.810.22321420.17432649X-RAY DIFFRACTION99.01
2.81-3.090.2171380.17892682X-RAY DIFFRACTION98.64
3.09-3.540.17861580.1642678X-RAY DIFFRACTION99.82
3.54-4.460.19331490.1582685X-RAY DIFFRACTION99.26
4.46-44.370.20811460.19142720X-RAY DIFFRACTION97.92

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