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- PDB-9gkx: Crystal Structure of Rhizorhabdus wittichii Dimethoate hydrolase ... -

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Basic information

Entry
Database: PDB / ID: 9gkx
TitleCrystal Structure of Rhizorhabdus wittichii Dimethoate hydrolase (DmhA) in complex with SAHA
ComponentsDimethoate hydrolase
KeywordsHYDROLASE / Inhibitor / SAHA / Deacetylase / Deacylase
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) / OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE / Dimethoate hydrolase
Similarity search - Component
Biological speciesRhizorhabdus wittichii DC-6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsGraf, L.G. / Lammers, M. / Schulze, S. / Palm, G.J.
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)164,50016
Polymers163,2654
Non-polymers1,23512
Water32,0671780
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16750 Å2
ΔGint-218 kcal/mol
Surface area41790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.12, 144.96, 92.66
Angle α, β, γ (deg.)90, 91.81, 90
Int Tables number5
Space group name H-MC121

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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: His6x-Tag fusion-protein / Source: (gene. exp.) Rhizorhabdus wittichii DC-6 (bacteria) / Strain: DC-6 / KACC 16600 / Gene: dmhA / Plasmid: pET-45b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A067XIQ6

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Non-polymers , 5 types, 1792 molecules

#2: Chemical ChemComp-SHH / OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE / SAHA


Mass: 264.320 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID)


Mass: 144.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1780 / 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: 2.85 Å3/Da / Density % sol: 56.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting 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: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 174428 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / CC1/2: 0.994 / Rrim(I) all: 0.229 / Rsym value: 0.21 / Χ2: 0.99 / Net I/σ(I): 7.68
Reflection shellResolution: 1.75→1.86 Å / Num. unique obs: 28058 / CC1/2: 0.488 / Χ2: 0.9 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSJun 30, 2023 BUILT=20230630data reduction
XDSJun 30, 2023 BUILT=20230630data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→46.31 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1901 2101 -
Rwork0.1625 --
obs0.1629 174373 99.7 %
Refinement stepCycle: LAST / Resolution: 1.75→46.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11028 0 66 1780 12874

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