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- PDB-8rqp: In meso structure of the alginate exporter, AlgE, from Pseudomona... -

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Basic information

Entry
Database: PDB / ID: 8rqp
TitleIn meso structure of the alginate exporter, AlgE, from Pseudomonas aeruginosa in 7.10 monoacylglycerol
ComponentsAlginate production protein AlgE
KeywordsMEMBRANE PROTEIN / Alginate exporter
Function / homologyAlginate export domain / : / Alginate export / alginic acid biosynthetic process / cell outer membrane / : / : / CITRIC ACID / Alginate production protein AlgE
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSmithers, L. / Boland, C. / Krawinski, P. / Caffrey, M.
Funding support Ireland, 4items
OrganizationGrant numberCountry
Science Foundation Ireland16/IA/4435 Ireland
Science Foundation Ireland22/FFP-A/10278 Ireland
Irish Research CouncilGOIPG/2019/3074 Ireland
Irish Research CouncilGOIPD/2021/40 Ireland
CitationJournal: Cryst.Growth Des. / Year: 2024
Title: 7.10 MAG. A Novel Host Monoacylglyceride for In Meso (Lipid Cubic Phase) Crystallization of Membrane Proteins.
Authors: Krawinski, P. / Smithers, L. / van Dalsen, L. / Boland, C. / Ostrovitsa, N. / Perez, J. / Caffrey, M.
History
DepositionJan 19, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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)58,37020
Polymers53,5021
Non-polymers4,86819
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-38 kcal/mol
Surface area21270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.358, 74.546, 115.913
Angle α, β, γ (deg.)90.000, 102.490, 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 , 9 types, 253 molecules

#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical
ChemComp-A1H2K / 7.10 monoacylglycerol (S-form) / [(2S)-2,3-bis(oxidanyl)propyl] (E)-heptadec-7-enoate


Mass: 342.513 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C20H38O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-A1H52 / 7.10 monoacylglycerol (R-form) / [(2R)-2,3-bis(oxidanyl)propyl] (E)-heptadec-7-enoate


Mass: 342.513 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H38O4
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 45.6 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 34-41 %(v/v) PEG400, 100 mM LiSO4, and 100 mM Na-Citrate at pH 5.6 and 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9779 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 1.45→39.4 Å / Num. obs: 61350 / % possible obs: 90.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 15.48 Å2 / CC1/2: 0.99 / Net I/σ(I): 7.2
Reflection shellResolution: 1.45→1.5 Å / Num. unique obs: 3068 / CC1/2: 0.273

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→39.37 Å / SU ML: 0.164 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.8835
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2229 3103 5.07 %
Rwork0.1898 58151 -
obs0.1915 61254 72.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.46 Å2
Refinement stepCycle: LAST / Resolution: 1.45→39.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3635 0 304 234 4173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01244085
X-RAY DIFFRACTIONf_angle_d1.27255464
X-RAY DIFFRACTIONf_chiral_restr0.257534
X-RAY DIFFRACTIONf_plane_restr0.0118706
X-RAY DIFFRACTIONf_dihedral_angle_d15.7305740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.470.407610.288570X-RAY DIFFRACTION1.81
1.47-1.490.2941100.242153X-RAY DIFFRACTION4.38
1.49-1.520.2592240.255288X-RAY DIFFRACTION8.17
1.52-1.550.2998350.2544572X-RAY DIFFRACTION15.96
1.55-1.580.3116560.2642983X-RAY DIFFRACTION27.38
1.58-1.610.2639870.25981629X-RAY DIFFRACTION44.14
1.61-1.640.30791370.27152292X-RAY DIFFRACTION64.07
1.64-1.680.2741570.25662858X-RAY DIFFRACTION77.67
1.68-1.730.29211500.25383100X-RAY DIFFRACTION85.26
1.73-1.770.29381550.24863215X-RAY DIFFRACTION88.2
1.77-1.820.34061570.23813391X-RAY DIFFRACTION92.06
1.82-1.880.24882020.21793416X-RAY DIFFRACTION93.71
1.88-1.950.24922040.20083433X-RAY DIFFRACTION94.59
1.95-2.030.19881860.18833490X-RAY DIFFRACTION95.8
2.03-2.120.21871970.17683641X-RAY DIFFRACTION99.71
2.12-2.230.21541890.17523669X-RAY DIFFRACTION99.92
2.23-2.370.21421870.17273642X-RAY DIFFRACTION99.97
2.37-2.560.19321810.17793664X-RAY DIFFRACTION99.79
2.56-2.810.22581880.19183662X-RAY DIFFRACTION99.72
2.81-3.220.23422040.18183645X-RAY DIFFRACTION99.12
3.22-4.060.17892150.16123569X-RAY DIFFRACTION97.58
4.06-39.370.21761810.18633769X-RAY DIFFRACTION99.67
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)
10.9494355865260.1822352474490.01143413430593.97495562187-3.453822300693.049804939880.01362524198890.0571278019268-0.0253324202884-0.0717418211064-0.0120434609012-0.02571964307720.0818447682735-0.00129054417806-0.01770559919320.110504775593-0.02201161864810.003463480591440.110157434828-0.05969023603090.1218744817785.79160536573-4.6162391912438.5461047143
22.07285023082-1.645623467590.8649317543222.82705656753-0.9858308924670.946253833840.1162229132880.1515058055930.121435608719-0.219741739181-0.188812822503-0.0717383351163-0.03594892852160.162526140810.09795334912220.0812415128543-0.0339871125199-0.02268157883210.132135778039-0.004918815479450.1172016802583.66816734871-10.546097657332.0454405709
31.300480338940.107388463279-0.008147079268720.74605277935-0.09830098469230.6826858808060.0269435394612-0.02354202147750.05069098809090.0557323815223-0.00922873874581-0.0101982795727-0.04091498972670.0470964807856-0.005932918166240.0641277818401-0.0116585004681-0.005136899137850.0518272745251-0.003416537212650.077274252992120.7371568594-13.5341131533.843174359
40.5470751665850.189177034217-0.2079346356481.484355581981.361676264452.010228956180.01542732282690.0828039650555-0.00922416061971-0.0684122307947-0.1100105260970.01035878979280.0122117353488-0.2179870302260.1007708591640.0517911096789-0.0136584517784-0.001006257428790.1137274962020.008396438223080.083710151707325.3583114434-1.8134239951522.1102927248
51.9825126625-0.327340438066-1.352356412261.168007421270.6002837731973.392712286540.01589628753570.03346626450450.000460039672449-0.121237039352-0.07338218554830.04611701148730.003780736515410.0212079871940.04021730489830.0620198386579-0.0191968297851-0.02381491169360.0628836449614-0.005437291716920.12522352739817.99058007948.5967548519427.7130966071
62.157470773581.32313737302-2.149609197972.4421701524-1.625428072572.238477658180.02715140540020.01432526878480.145464098673-0.03678674356690.009593486702260.0917632774920.0348965335680.00414166215035-0.07230837027970.0731374756909-0.00792455314147-0.04898954818210.113665641475-0.007737082261310.1341230502647.012095421138.3564125249132.3963561978
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 13 through 65 )13 - 651 - 53
22chain 'A' and (resid 66 through 123 )66 - 12354 - 102
33chain 'A' and (resid 124 through 230 )124 - 230103 - 209
44chain 'A' and (resid 231 through 350 )231 - 350210 - 329
55chain 'A' and (resid 351 through 424 )351 - 424330 - 403
66chain 'A' and (resid 425 through 490 )425 - 490404 - 459

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