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- PDB-6twk: Substrate bound structure of the Ectoine utilization protein EutD... -

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Basic information

Entry
Database: PDB / ID: 6twk
TitleSubstrate bound structure of the Ectoine utilization protein EutD (DoeA) from Halomonas elongata
ComponentsEctoine hydrolase DoeA
KeywordsHYDROLASE / Pita bread / ectoine degradation
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 / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like
Similarity search - Domain/homology
Chem-4CS / Chem-P4B / Putative peptidase / Ectoine hydrolase
Similarity search - Component
Biological speciesHalomonas elongata (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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
DepositionJan 13, 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
A: Ectoine hydrolase DoeA
B: Ectoine hydrolase DoeA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2954
Polymers89,9902
Non-polymers3042
Water9,422523
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Analytical SEC + MALS/RI
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-30 kcal/mol
Surface area28190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.200, 158.200, 122.320
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-557-

HOH

21A-714-

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-P4B / (2~{R})-4-azanyl-2-[[(1~{S})-1-oxidanylethyl]amino]butanoic acid


Mass: 162.187 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H14N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-4CS / (4S)-2-METHYL-1,4,5,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC ACID / ECTOINE


Mass: 142.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C6H10N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / 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: 4.17 Å3/Da / Density % sol: 70.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M trisodium citrate, 20% (wt/vol) PEG 3350 / PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873127 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873127 Å / Relative weight: 1
ReflectionResolution: 2.2→48.42 Å / Num. obs: 78809 / % possible obs: 99.96 % / Redundancy: 8.9 % / Biso Wilson estimate: 34.55 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1474 / Net I/σ(I): 10.69
Reflection shellResolution: 2.2→2.279 Å / Rmerge(I) obs: 1.466 / Mean I/σ(I) obs: 1.65 / Num. unique obs: 6599 / CC1/2: 0.583

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Coot0.8.9.2model building
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TWJ

6twj


Resolution: 2.25→43.88 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1937 --
Rwork0.1687 --
obs-77728 98.48 %
Displacement parametersBiso mean: 38.52 Å2
Refinement stepCycle: LAST / Resolution: 2.25→43.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6282 0 21 523 6826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00826492
X-RAY DIFFRACTIONf_angle_d0.95428827
X-RAY DIFFRACTIONf_chiral_restr0.0582906
X-RAY DIFFRACTIONf_plane_restr0.00621152
X-RAY DIFFRACTIONf_dihedral_angle_d17.61592375

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