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- PDB-6twl: Apo structure of the Ectoine utilization protein EutE (DoeB) from... -

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Basic information

Entry
Database: PDB / ID: 6twl
TitleApo structure of the Ectoine utilization protein EutE (DoeB) from Ruegeria pomeroyi
ComponentsN-acetyl-L-2,4-diaminobutyric acid deacetylase
KeywordsHYDROLASE / Pita bread / ectoine degradation
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / hydrolase activity, acting on ester bonds / metal ion binding
Similarity search - Function
N-alpha-acetyl diaminobutyric acid deacetylase-like / N-alpha-acetyl diaminobutyrate deacetylase DoeB / Succinylglutamate desuccinylase/aspartoacylase / Succinylglutamate desuccinylase / Aspartoacylase family / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
N-acetyl-L-2,4-diaminobutyric acid deacetylase
Similarity search - Component
Biological speciesRuegeria pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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: N-acetyl-L-2,4-diaminobutyric acid deacetylase


Theoretical massNumber of molelcules
Total (without water)35,1471
Polymers35,1471
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13850 Å2
2
A: N-acetyl-L-2,4-diaminobutyric acid deacetylase
x 6


Theoretical massNumber of molelcules
Total (without water)210,8826
Polymers210,8826
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_555-y,-x,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_545x,x-y-1,-z+1/21
Buried area16310 Å2
ΔGint-55 kcal/mol
Surface area66780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.190, 99.190, 134.620
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2

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Components

#1: Protein N-acetyl-L-2,4-diaminobutyric acid deacetylase


Mass: 35146.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3) (bacteria)
Gene: doeB, SPO1139 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5LUB5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: 0.1 M Bicine pH 9.0, 20% (wt/vol) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97242 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 1.99→46.54 Å / Num. obs: 27066 / % possible obs: 99.48 % / Redundancy: 21 % / Biso Wilson estimate: 61.44 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.0626 / Net I/σ(I): 23
Reflection shellResolution: 1.99→2.06 Å / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2612 / CC1/2: 0.551

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CDX

3cdx


Resolution: 2→46.54 Å / SU ML: 0.3627 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 41.4651
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2949 1350 5.01 %
Rwork0.2447 25613 -
obs0.2471 26963 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.66 Å2
Refinement stepCycle: LAST / Resolution: 2→46.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2327 0 0 14 2341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00482376
X-RAY DIFFRACTIONf_angle_d0.91313226
X-RAY DIFFRACTIONf_chiral_restr0.0664367
X-RAY DIFFRACTIONf_plane_restr0.006424
X-RAY DIFFRACTIONf_dihedral_angle_d8.1452328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.070.51841310.48242481X-RAY DIFFRACTION98.86
2.07-2.150.50971320.41562518X-RAY DIFFRACTION99.74
2.15-2.250.44871320.41892498X-RAY DIFFRACTION98.98
2.25-2.370.37161300.33192484X-RAY DIFFRACTION98.72
2.37-2.520.35281330.30732520X-RAY DIFFRACTION99.44
2.52-2.710.34991340.29832532X-RAY DIFFRACTION99.59
2.71-2.990.31591360.28862571X-RAY DIFFRACTION99.78
2.99-3.420.35071360.27662587X-RAY DIFFRACTION99.85
3.42-4.310.27951380.22232625X-RAY DIFFRACTION100
4.31-46.540.24731480.20512797X-RAY DIFFRACTION99.97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.46305524758-0.423369995415-0.6007375205313.3784841617-0.2576629820353.48608874598-0.0736020360214-0.140385084179-0.2124217889470.1189278232570.0127267541179-0.1881993652210.4684897332050.02182569559570.05293693322780.6904021599480.00805140724325-0.0547598809110.641689953883-0.06687412440490.59762918445222.6284393529-38.344763437115.5715812437
22.438821405011.10420542042-0.2389478208713.14160982262.490148982632.24378012878-0.2493626050640.3383326376590.193418894399-0.3228849323760.18660695151-0.338967006556-0.2384512582910.3633186456110.03552832962820.6323715505730.0171641213271-0.06749036159220.831953989175-0.02086460390580.64669303718227.1029401508-24.289321841811.3281147527
30.8226199299581.048362909470.8501978034012.991986261731.871155912391.15984823832-0.08047950834310.05634646939080.305277046888-0.150393559289-0.07059671455960.443772840449-0.176303245719-0.08953518172960.1819583854980.6226660457190.0357098139581-0.1114558055550.727483204916-0.03594503637680.6662823734221.4421332519-14.502431326718.5981689597
42.37538453940.8218078191340.2238319413093.574162046440.2270421615743.16422486991-0.08898281310970.4390563523550.272297868694-0.02056322458740.02548747950710.0341032385856-0.3532650994590.7124925699480.006838605964410.6491051194270.0242714236199-0.08217170906480.643420457721-0.0008677113116180.64787941874234.480278811-2.3086862842526.9467595861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 87 )
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 193 )
3X-RAY DIFFRACTION3chain 'A' and (resid 194 through 281 )
4X-RAY DIFFRACTION4chain 'A' and (resid 282 through 328 )

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