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- PDB-8pz4: Structure of alginate transporter, AlgE, solved at wavelength 2.755 A -

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Basic information

Entry
Database: PDB / ID: 8pz4
TitleStructure of alginate transporter, AlgE, solved at wavelength 2.755 A
ComponentsAlginate production protein AlgE
KeywordsMEMBRANE PROTEIN / transporter
Function / homologyAlginate export domain / : / Alginate export / alginic acid biosynthetic process / cell outer membrane / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / CITRATE ANION / Alginate production protein AlgE
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.77 Å
AuthorsDuman, R. / El Omari, K. / Mykhaylyk, V. / Orr, C. / Wagner, A. / Vogeley, L. / Brown, D.G.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Diamond Light Source United Kingdom
CitationJournal: Commun Chem / Year: 2023
Title: Experimental phasing opportunities for macromolecular crystallography at very long wavelengths.
Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / ...Authors: El Omari, K. / Duman, R. / Mykhaylyk, V. / Orr, C.M. / Latimer-Smith, M. / Winter, G. / Grama, V. / Qu, F. / Bountra, K. / Kwong, H.S. / Romano, M. / Reis, R.I. / Vogeley, L. / Vecchia, L. / Owen, C.D. / Wittmann, S. / Renner, M. / Senda, M. / Matsugaki, N. / Kawano, Y. / Bowden, T.A. / Moraes, I. / Grimes, J.M. / Mancini, E.J. / Walsh, M.A. / Guzzo, C.R. / Owens, R.J. / Jones, E.Y. / Brown, D.G. / Stuart, D.I. / Beis, K. / Wagner, A.
History
DepositionJul 26, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alginate production protein AlgE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,70122
Polymers53,5021
Non-polymers5,19921
Water3,405189
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.350, 74.690, 115.900
Angle α, β, γ (deg.)90.000, 102.480, 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 (bacteria) / Gene: algE, alg76, PA3544 / Production host: Escherichia coli (E. coli) / References: UniProt: P18895

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Non-polymers , 8 types, 210 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H31NO / Feature type: SUBJECT OF INVESTIGATION / Comment: LDAO, detergent*YM
#6: Chemical ChemComp-78M / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL


Mass: 314.460 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H34O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-78N / (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL (2R)


Mass: 314.460 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H34O4 / Feature type: SUBJECT OF INVESTIGATION
#8: 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.26 Å3/Da / Density % sol: 45.69 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 7.5
Details: 0.1 M TRIS-HCL, PH 7.5, 0.1 M SODIUM CITRATE, 18 %(W/V) PEG 400. PROTEIN WAS MIXED WITH 7.8 MAG AT RATIO 1:1 (W:W) TO FORM CUBIC PHASE.

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 2.755 Å
DetectorType: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Aug 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2.755 Å / Relative weight: 1
ReflectionResolution: 1.77→56.58 Å / Num. obs: 88023 / % possible obs: 96.76 % / Redundancy: 26.7 % / Biso Wilson estimate: 23.7 Å2 / CC1/2: 0.999 / Net I/σ(I): 27.32
Reflection shellResolution: 1.77→1.833 Å / Num. unique obs: 4019 / CC1/2: 0.903

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.77→56.58 Å / SU ML: 0.2107 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.6529
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2339 3998 4.54 %
Rwork0.1877 84025 -
obs0.1897 88023 96.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.43 Å2
Refinement stepCycle: LAST / Resolution: 1.77→56.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3683 0 286 189 4158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00684063
X-RAY DIFFRACTIONf_angle_d0.97385429
X-RAY DIFFRACTIONf_chiral_restr0.0602529
X-RAY DIFFRACTIONf_plane_restr0.0071707
X-RAY DIFFRACTIONf_dihedral_angle_d16.866684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.790.38421150.33442133X-RAY DIFFRACTION71.3
1.79-1.810.33071590.33312802X-RAY DIFFRACTION91.62
1.81-1.840.39511150.31882741X-RAY DIFFRACTION92.76
1.84-1.860.31361470.26612780X-RAY DIFFRACTION93.37
1.86-1.890.29011420.27582906X-RAY DIFFRACTION93.78
1.89-1.910.26281490.24912778X-RAY DIFFRACTION93.54
1.91-1.940.26181510.22372736X-RAY DIFFRACTION94.25
1.94-1.970.25641290.22282919X-RAY DIFFRACTION94.37
1.97-20.2211300.19522807X-RAY DIFFRACTION94.04
2-2.040.25581380.19982911X-RAY DIFFRACTION95.13
2.04-2.080.22071230.19712840X-RAY DIFFRACTION95.37
2.08-2.110.25311540.1972895X-RAY DIFFRACTION95.79
2.11-2.160.21891170.18812876X-RAY DIFFRACTION96.49
2.16-2.210.21741560.19462921X-RAY DIFFRACTION96.61
2.21-2.260.29311130.18452978X-RAY DIFFRACTION97.14
2.26-2.310.25081290.17842930X-RAY DIFFRACTION98.11
2.31-2.380.18451210.17693007X-RAY DIFFRACTION98.12
2.38-2.450.23161350.18922973X-RAY DIFFRACTION98.79
2.45-2.520.25091540.18962951X-RAY DIFFRACTION98.95
2.52-2.610.22031470.19663077X-RAY DIFFRACTION99.6
2.61-2.720.22881470.19892930X-RAY DIFFRACTION99.81
2.72-2.840.25281270.19923057X-RAY DIFFRACTION99.81
2.84-2.990.23781470.192989X-RAY DIFFRACTION99.94
2.99-3.180.27841770.1852978X-RAY DIFFRACTION99.97
3.18-3.430.22171520.16692992X-RAY DIFFRACTION100
3.43-3.770.21541460.15292998X-RAY DIFFRACTION99.87
3.77-4.320.19791280.15963069X-RAY DIFFRACTION99.94
4.32-5.440.1951060.16373024X-RAY DIFFRACTION99.97
5.44-56.580.22051440.20153027X-RAY DIFFRACTION99.84
Refinement TLS params.Method: refined / Origin x: 15.8123825024 Å / Origin y: 10.0349664802 Å / Origin z: 30.5498486659 Å
111213212223313233
T0.180435383703 Å2-0.0193587390854 Å2-0.00164243330631 Å2-0.119820321083 Å2-0.0010031151353 Å2--0.106273920855 Å2
L0.585339122572 °20.117243228696 °2-0.0674421736223 °2-0.526186293204 °20.082018897314 °2--0.298652146918 °2
S0.0184698428554 Å °0.05504407922 Å °0.035385189188 Å °-0.0380895020223 Å °-0.0164093135845 Å °0.0299748680798 Å °-0.0251597196481 Å °-0.0195134852187 Å °-0.00935522569152 Å °
Refinement TLS groupSelection details: all

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