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Basic information

Entry
Database: PDB / ID: 5iyu
TitleAlgE_CIM
ComponentsAlginate production protein AlgE
KeywordsMEMBRANE PROTEIN / alginate transporter
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
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Alginate production protein AlgE
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMa, P. / Weichert, D.
CitationJournal: Nat Protoc / Year: 2017
Title: The cubicon method for concentrating membrane proteins in the cubic mesophase.
Authors: Ma, P. / Weichert, D. / Aleksandrov, L.A. / Jensen, T.J. / Riordan, J.R. / Liu, X. / Kobilka, B.K. / Caffrey, M.
History
DepositionMar 24, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Structure summary
Revision 1.2Aug 30, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _citation.country ..._chem_comp.pdbx_synonyms / _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)56,1177
Polymers54,4811
Non-polymers1,6356
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint9 kcal/mol
Surface area19910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.830, 73.390, 114.530
Angle α, β, γ (deg.)90.00, 101.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alginate production protein AlgE


Mass: 54481.355 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 , 5 types, 44 molecules

#2: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#3: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H40O4
#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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.14 Å3/Da / Density % sol: 42.65 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase
Details: 38 %(v/v) PEG 400, 0.1 M NaCitrate pH 5.6 and 0.1 M bis-tris pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9993 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9993 Å / Relative weight: 1
ReflectionResolution: 2.7→44.32 Å / Num. obs: 12694 / % possible obs: 99.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 4.7
Reflection shellRmerge(I) obs: 0.598

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Processing

Software
NameVersionClassification
PHENIX(dev_2283: ???)refinement
xia2data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AFK

4afk


Resolution: 2.7→44.32 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.55
RfactorNum. reflection% reflection
Rfree0.2825 579 4.56 %
Rwork0.2232 --
obs0.2261 12693 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→44.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3407 0 81 38 3526
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033567
X-RAY DIFFRACTIONf_angle_d0.5844814
X-RAY DIFFRACTIONf_dihedral_angle_d15.5192014
X-RAY DIFFRACTIONf_chiral_restr0.043483
X-RAY DIFFRACTIONf_plane_restr0.003635
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7002-2.97190.3551480.27722983X-RAY DIFFRACTION99
2.9719-3.40190.3371460.26862989X-RAY DIFFRACTION99
3.4019-4.28580.28031470.19683044X-RAY DIFFRACTION100
4.2858-44.320.23191380.20733098X-RAY DIFFRACTION99

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