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- PDB-5onn: Crystal Structure of Ectoine Synthase from P. lautus -

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Basic information

Entry
Database: PDB / ID: 5onn
TitleCrystal Structure of Ectoine Synthase from P. lautus
ComponentsL-ectoine synthase
KeywordsMETAL BINDING PROTEIN / Ectoine / synthase / osmolyte
Function / homology
Function and homology information


ectoine synthase / ectoine synthase activity / ectoine biosynthetic process / metal ion binding
Similarity search - Function
Ectoine synthase / Ectoine synthase / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
(2~{S})-4-acetamido-2-azanyl-butanoic acid / : / L-ectoine synthase / L-ectoine synthase
Similarity search - Component
Biological speciesPaenibacillus lautus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBremer, E.
CitationJournal: Sci Rep / Year: 2019
Title: Illuminating the catalytic core of ectoine synthase through structural and biochemical analysis.
Authors: Czech, L. / Hoppner, A. / Kobus, S. / Seubert, A. / Riclea, R. / Dickschat, J.S. / Heider, J. / Smits, S.H.J. / Bremer, E.
History
DepositionAug 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: L-ectoine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7573
Polymers15,5411
Non-polymers2162
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.910, 70.910, 68.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

21A-420-

HOH

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Components

#1: Protein L-ectoine synthase / N-acetyldiaminobutyrate dehydratase


Mass: 15540.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus lautus (bacteria) / Gene: ectC, BK123_26285 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A1R1AV52, UniProt: A0A2A5LBI6*PLUS, ectoine synthase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-9YT / (2~{S})-4-acetamido-2-azanyl-butanoic acid


Mass: 160.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12N2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 3.2 Å3/Da / Density % sol: 61.57 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 4.2
Details: 0.2 M ammonium sulfate, 0.1 M phosphate citrate pH 4.2, 20% (v/v) PEG 300, 10% (v/v) glycerol.
PH range: 4.0-5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.988 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 1.2→45.737 Å / Num. obs: 53471 / % possible obs: 91.93 % / Redundancy: 20 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BXX
Resolution: 1.4→45.737 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.31
RfactorNum. reflection% reflection
Rfree0.1992 1447 3.77 %
Rwork0.1822 --
obs0.1828 38418 96.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→45.737 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1088 0 12 162 1262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011141
X-RAY DIFFRACTIONf_angle_d1.6511553
X-RAY DIFFRACTIONf_dihedral_angle_d14413
X-RAY DIFFRACTIONf_chiral_restr0.084171
X-RAY DIFFRACTIONf_plane_restr0.011199
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.45010.29521370.22853613X-RAY DIFFRACTION95
1.4501-1.50810.21891400.20883593X-RAY DIFFRACTION96
1.5081-1.57680.21351420.20083617X-RAY DIFFRACTION96
1.5768-1.65990.23511450.19123638X-RAY DIFFRACTION96
1.6599-1.76390.21391430.1923639X-RAY DIFFRACTION97
1.7639-1.90010.19541450.18153703X-RAY DIFFRACTION97
1.9001-2.09130.1721450.17063716X-RAY DIFFRACTION98
2.0913-2.39390.1881470.16773745X-RAY DIFFRACTION98
2.3939-3.0160.20111490.18263806X-RAY DIFFRACTION99
3.016-45.76150.19511540.18113901X-RAY DIFFRACTION98

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