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- PDB-4xnk: X-ray structure of AlgE1 -

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Basic information

Entry
Database: PDB / ID: 4xnk
TitleX-ray structure of AlgE1
ComponentsAlginate production protein AlgE
KeywordsTRANSPORT PROTEIN / AlgE alginate export protein
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
(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / Alginate production protein AlgE
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMa, P. / Huang, C.Y. / Olieric, V. / Diederichs, K. / Wang, M. / Caffrey, M.
Funding support Ireland, United States, Belgium, 3items
OrganizationGrant numberCountry
Science Foundation Ireland12/IA/1255 Ireland
National Institutes of HealthGM75915, P50GM073210, U54GM094599 United States
Belgian National Funds for Scientific ResearchWELBIO CR-2012S-04 Belgium
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: In meso in situ serial X-ray crystallography of soluble and membrane proteins.
Authors: Huang, C.Y. / Olieric, V. / Ma, P. / Panepucci, E. / Diederichs, K. / Wang, M. / Caffrey, M.
History
DepositionJan 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Jan 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 / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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 production protein AlgE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,19810
Polymers54,4811
Non-polymers1,7179
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-11 kcal/mol
Surface area20620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.010, 74.340, 184.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 , 6 types, 35 molecules

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


Mass: 229.402 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#3: 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.: 1 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#4: Chemical ChemComp-78M / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL


Mass: 314.460 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O4
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.34 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 450 mM NH4Cl, 21 %(v/v) PEG 400, 100 mM MES buffer pH 6.5

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 16066 / % possible obs: 94.3 % / Redundancy: 5.6 % / Biso Wilson estimate: 72.28 Å2 / Net I/σ(I): 4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.1 / % possible all: 96

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4AFK

4afk


Resolution: 2.8→47.42 Å / Cor.coef. Fo:Fc: 0.8269 / Cor.coef. Fo:Fc free: 0.7586 / SU R Cruickshank DPI: 0.812 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.836 / SU Rfree Blow DPI: 0.358 / SU Rfree Cruickshank DPI: 0.363
RfactorNum. reflection% reflectionSelection details
Rfree0.2738 1003 6.24 %RANDOM
Rwork0.2261 ---
obs0.2291 16066 94.5 %-
Displacement parametersBiso mean: 52.59 Å2
Baniso -1Baniso -2Baniso -3
1-14.1388 Å20 Å20 Å2
2---28.9518 Å20 Å2
3---14.8131 Å2
Refine analyzeLuzzati coordinate error obs: 0.371 Å
Refinement stepCycle: 1 / Resolution: 2.8→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3347 0 97 26 3470
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083547HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.074776HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1239SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes99HARMONIC2
X-RAY DIFFRACTIONt_gen_planes514HARMONIC5
X-RAY DIFFRACTIONt_it3519HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.64
X-RAY DIFFRACTIONt_other_torsion20.26
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion424SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3242SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3207 193 6.65 %
Rwork0.2406 2709 -
all0.246 2902 -
obs--94.5 %

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