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- PDB-5d5d: In meso in situ serial X-ray crystallography structure of AlgE at... -

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Basic information

Entry
Database: PDB / ID: 5d5d
TitleIn meso in situ serial X-ray crystallography structure of AlgE at 100 K
ComponentsAlginate production protein AlgE
KeywordsTRANSPORT PROTEIN / Beta-Barrel Membrane Proteins / 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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMa, P. / Huang, C.-Y. / Olieric, V. / Diederichs, K. / Wang, M. / Caffrey, M.
Funding support Ireland, Belgium, 2items
OrganizationGrant numberCountry
Science Foundation Ireland12/IA/1255 Ireland
Belgian National Funds for Scientific ResearchWELBIO CR-2012S-04 Belgium
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures.
Authors: Huang, C.Y. / Olieric, V. / Ma, P. / Howe, N. / Vogeley, L. / Liu, X. / Warshamanage, R. / Weinert, T. / Panepucci, E. / Kobilka, B. / Diederichs, K. / Wang, M. / Caffrey, M.
History
DepositionAug 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)59,18520
Polymers54,4811
Non-polymers4,70419
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint15 kcal/mol
Surface area18740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.330, 66.350, 176.840
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 (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Gene: algE, alg76, PA3544 / Production host: Escherichia coli (E. coli) / References: UniProt: P18895

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Non-polymers , 7 types, 42 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#5: 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 / Polyethylene glycol


Mass: 398.489 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#6: Chemical ChemComp-78M / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL


Mass: 314.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O4
#7: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 20% Peg 400, 0.1 M Mes pH 6.0, 0.4 M K thiocyanate, 0.02 M dimannuronate
PH range: 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 20520 / % possible obs: 92.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 59.11 Å2 / Net I/σ(I): 5.98
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.45 / % possible all: 90.8

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Processing

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

4afk


Resolution: 2.4→25.22 Å / Cor.coef. Fo:Fc: 0.9071 / Cor.coef. Fo:Fc free: 0.8731 / SU R Cruickshank DPI: 0.391 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.386 / SU Rfree Blow DPI: 0.258 / SU Rfree Cruickshank DPI: 0.263
RfactorNum. reflection% reflection
Rfree0.2598 999 4.87 %
Rwork0.2192 --
obs0.2211 20520 92.83 %
Displacement parametersBiso mean: 50.44 Å2
Baniso -1Baniso -2Baniso -3
1-2.0851 Å20 Å20 Å2
2---15.6869 Å20 Å2
3---13.6017 Å2
Refine analyzeLuzzati coordinate error obs: 0.313 Å
Refinement stepCycle: 1 / Resolution: 2.4→25.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3222 0 233 23 3478
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013522HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.224714HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1264SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes91HARMONIC2
X-RAY DIFFRACTIONt_gen_planes498HARMONIC5
X-RAY DIFFRACTIONt_it3522HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.69
X-RAY DIFFRACTIONt_other_torsion18.48
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion404SEMIHARMONIC5
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_contact4136SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.53 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3125 147 4.98 %
Rwork0.2373 2806 -
all0.2412 2953 -
obs--92.83 %

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