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- PDB-9gkw: Crystal Structure of Dimethoate hydrolase (DmhA) of Rhizorhabdus ... -

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Basic information

Entry
Database: PDB / ID: 9gkw
TitleCrystal Structure of Dimethoate hydrolase (DmhA) of Rhizorhabdus wittichii in complex with octanoic acid
ComponentsDimethoate hydrolase
KeywordsHYDROLASE / Deacetylase / Deacylase / Octanoic acid
Function / homology
Function and homology information


histone deacetylase activity / epigenetic regulation of gene expression / hydrolase activity
Similarity search - Function
: / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily
Similarity search - Domain/homology
: / OCTANOIC ACID (CAPRYLIC ACID) / Dimethoate hydrolase
Similarity search - Component
Biological speciesRhizorhabdus wittichii DC-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGraf, L.G. / Schulze, S. / Palm, G.J. / Lammers, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)LA2984/6-1 Germany
German Research Foundation (DFG)LA2984/8-1 Germany
CitationJournal: Nat Commun / Year: 2024
Title: Distribution and diversity of classical deacylases in bacteria.
Authors: Graf, L.G. / Moreno-Yruela, C. / Qin, C. / Schulze, S. / Palm, G.J. / Schmoker, O. / Wang, N. / Hocking, D.M. / Jebeli, L. / Girbardt, B. / Berndt, L. / Dorre, B. / Weis, D.M. / Janetzky, M. ...Authors: Graf, L.G. / Moreno-Yruela, C. / Qin, C. / Schulze, S. / Palm, G.J. / Schmoker, O. / Wang, N. / Hocking, D.M. / Jebeli, L. / Girbardt, B. / Berndt, L. / Dorre, B. / Weis, D.M. / Janetzky, M. / Albrecht, D. / Zuhlke, D. / Sievers, S. / Strugnell, R.A. / Olsen, C.A. / Hofmann, K. / Lammers, M.
History
DepositionAug 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dimethoate hydrolase
B: Dimethoate hydrolase
C: Dimethoate hydrolase
D: Dimethoate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)165,20925
Polymers163,2654
Non-polymers1,94421
Water19,8171100
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19150 Å2
ΔGint-223 kcal/mol
Surface area42040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.616, 144.034, 92.959
Angle α, β, γ (deg.)90.000, 92.119, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-751-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Dimethoate hydrolase


Mass: 40816.195 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: His6-tagged fusion-protein / Source: (gene. exp.) Rhizorhabdus wittichii DC-6 (bacteria) / Strain: DC-6 / Gene: dmhA / Plasmid: pET-45b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A067XIQ6

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Non-polymers , 5 types, 1121 molecules

#2: Chemical
ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID)


Mass: 144.211 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H16O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1100 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.71 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.2 M potassium fluoride pH 7.3 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97951 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 27, 2023 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.1→54.64 Å / Num. obs: 85350 / % possible obs: 84.7 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 21.95 Å2 / CC1/2: 0.988 / Rrim(I) all: 0.228 / Rsym value: 0.2 / Net I/σ(I): 8.26
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 4.47 % / Mean I/σ(I) obs: 2.12 / Num. unique obs: 14336 / CC1/2: 0.646 / Rrim(I) all: 0.964 / % possible all: 88.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→45.1 Å / SU ML: 0.2336 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1217
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2242 4547 5.35 %
Rwork0.1692 80431 -
obs0.1722 84978 84.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.24 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11059 0 102 1100 12261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007911560
X-RAY DIFFRACTIONf_angle_d0.986715744
X-RAY DIFFRACTIONf_chiral_restr0.05341720
X-RAY DIFFRACTIONf_plane_restr0.00932095
X-RAY DIFFRACTIONf_dihedral_angle_d16.63924151
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.32581370.25042571X-RAY DIFFRACTION81.1
2.12-2.150.28521540.21082835X-RAY DIFFRACTION90
2.15-2.170.27191670.20762816X-RAY DIFFRACTION89.36
2.17-2.20.2371440.21232858X-RAY DIFFRACTION89.21
2.2-2.230.28161370.21552847X-RAY DIFFRACTION89.29
2.23-2.260.562850.37562215X-RAY DIFFRACTION67.95
2.26-2.290.29091420.21172779X-RAY DIFFRACTION88.57
2.29-2.330.25861850.19672825X-RAY DIFFRACTION88.58
2.33-2.360.28171480.18692761X-RAY DIFFRACTION87.96
2.36-2.40.24661890.18392746X-RAY DIFFRACTION87.53
2.4-2.440.2661700.18242776X-RAY DIFFRACTION87.21
2.44-2.490.24211630.17912712X-RAY DIFFRACTION86.6
2.49-2.540.28861560.18362695X-RAY DIFFRACTION85.74
2.54-2.590.25651400.17072742X-RAY DIFFRACTION85.47
2.59-2.650.22371430.17712619X-RAY DIFFRACTION82.28
2.65-2.710.25641420.19582642X-RAY DIFFRACTION83.03
2.71-2.770.24011620.17912763X-RAY DIFFRACTION87.21
2.77-2.850.2371530.17242750X-RAY DIFFRACTION86.79
2.85-2.930.2441510.18192745X-RAY DIFFRACTION86.19
2.93-3.030.24391640.17042746X-RAY DIFFRACTION86.4
3.03-3.140.24581580.16712695X-RAY DIFFRACTION84.99
3.14-3.260.2321500.1722689X-RAY DIFFRACTION84.97
3.26-3.410.21621600.1712701X-RAY DIFFRACTION84.72
3.41-3.590.19371260.1612613X-RAY DIFFRACTION81.37
3.59-3.810.2051440.15082489X-RAY DIFFRACTION78.55
3.81-4.110.17921480.13972493X-RAY DIFFRACTION78.53
4.11-4.520.13681810.11562643X-RAY DIFFRACTION83.65
4.52-5.180.17581540.11532641X-RAY DIFFRACTION82.57
5.18-6.520.19211420.14492551X-RAY DIFFRACTION79.67
6.52-45.10.16811520.14032473X-RAY DIFFRACTION76.44

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