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- PDB-6yo9: Product bound structure of the Ectoine utilization protein EutD (... -

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Basic information

Entry
Database: PDB / ID: 6yo9
TitleProduct bound structure of the Ectoine utilization protein EutD (DoeA) from Halomonas elongata
ComponentsEctoine hydrolase DoeA
KeywordsHYDROLASE / EutE / ADABA / ectoine / compatible solutes
Function / homology
Function and homology information


ectoine hydrolase / ectoine catabolic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / Hydrolases; Acting on peptide bonds (peptidases) / hydrolase activity / cytoplasm
Similarity search - Function
Ectoine utilization protein EutD / : / Creatinase, N-terminal / Creatinase/Prolidase N-terminal domain / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 ...Ectoine utilization protein EutD / : / Creatinase, N-terminal / Creatinase/Prolidase N-terminal domain / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-P4B / Putative peptidase / Ectoine hydrolase
Similarity search - Component
Biological speciesHalomonas elongata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMais, C.-N. / Altegoer, F. / Bange, G.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Degradation of the microbial stress protectants and chemical chaperones ectoine and hydroxyectoine by a bacterial hydrolase-deacetylase complex.
Authors: Mais, C.N. / Hermann, L. / Altegoer, F. / Seubert, A. / Richter, A.A. / Wernersbach, I. / Czech, L. / Bremer, E. / Bange, G.
History
DepositionApr 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 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
B: Ectoine hydrolase DoeA
A: Ectoine hydrolase DoeA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,5917
Polymers89,9902
Non-polymers6015
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-29 kcal/mol
Surface area27620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.073, 157.073, 124.072
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-567-

HOH

21A-649-

HOH

31A-662-

HOH

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Components

#1: Protein Ectoine hydrolase DoeA / Putative peptidase


Mass: 44995.125 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halomonas elongata (bacteria) / Gene: doeA, A8U91_03446, DKQ62_09665 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1B8NWR1, UniProt: E1V7W1*PLUS, Hydrolases; Acting on peptide bonds (peptidases)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-P4B / (2~{R})-4-azanyl-2-[[(1~{S})-1-oxidanylethyl]amino]butanoic acid


Mass: 162.187 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O
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: 4.25 Å3/Da / Density % sol: 71.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M trisodium citrate, 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 16, 2019
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.399→50 Å / Num. obs: 60665 / % possible obs: 99.14 % / Redundancy: 14.7 % / Biso Wilson estimate: 46.24 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1901 / Rpim(I) all: 0.05096 / Net I/σ(I): 12.02
Reflection shellResolution: 2.399→2.484 Å / Num. unique obs: 5767 / CC1/2: 0.766

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TWJ

6twj


Resolution: 2.4→19.39 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2274 -5 %
Rwork0.1842 --
obs-60625 99.32 %
Displacement parametersBiso mean: 52.4 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6291 0 40 334 6665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00836516
X-RAY DIFFRACTIONf_angle_d0.95858854
X-RAY DIFFRACTIONf_chiral_restr0.1797909
X-RAY DIFFRACTIONf_plane_restr0.00621153
X-RAY DIFFRACTIONf_dihedral_angle_d18.70112383

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