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- PDB-9n2w: Dienelactone hydrolase family protein SaDLH from Solimonas aquatica -

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Basic information

Entry
Database: PDB / ID: 9n2w
TitleDienelactone hydrolase family protein SaDLH from Solimonas aquatica
ComponentsDienelactone hydrolase
KeywordsHYDROLASE / sulfinic acid / dienelactone / alpha/beta hydrolase
Function / homologyDienelactone hydrolase / Dienelactone hydrolase family / : / Alpha/Beta hydrolase fold / hydrolase activity / Dienelactone hydrolase
Function and homology information
Biological speciesSolimonas aquatica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSchnettler Fernandez, J.D.F. / Campbell, E.C. / Hollfelder, F.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Commission695669European Union
CitationJournal: To Be Published
Title: Metal-independent organophosphate hydrolysis in a protein family possessing a catalytic triad
Authors: Schnettler, J.D.F. / Campbell, E.C. / Khashiev, R. / Klein, J.O. / Hollfelder, F.
History
DepositionJan 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dienelactone hydrolase
B: Dienelactone hydrolase


Theoretical massNumber of molelcules
Total (without water)51,4552
Polymers51,4552
Non-polymers00
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.446, 76.408, 72.459
Angle α, β, γ (deg.)90.000, 107.770, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Dienelactone hydrolase


Mass: 25727.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solimonas aquatica (bacteria) / Gene: SAMN04488038_103247 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1H9CZH3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 55.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES 7.5 pH (Buffer) 4.3 M NaCl (Precipitant)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.9→69 Å / Num. obs: 41834 / % possible obs: 95.49 % / Redundancy: 1.9 % / Biso Wilson estimate: 24.7 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.04279 / Net I/σ(I): 7.1
Reflection shellResolution: 1.9→1.968 Å / Num. unique obs: 4118 / CC1/2: 0.924

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→69 Å / SU ML: 0.2504 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.0172
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2981 2110 5.04 %
Rwork0.2429 39724 -
obs0.2457 41834 95.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3630 0 0 142 3772
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083704
X-RAY DIFFRACTIONf_angle_d1.1485030
X-RAY DIFFRACTIONf_chiral_restr0.0551546
X-RAY DIFFRACTIONf_plane_restr0.0096676
X-RAY DIFFRACTIONf_dihedral_angle_d8.0354530
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.48591360.49442664X-RAY DIFFRACTION97.09
1.94-1.990.45591420.38822615X-RAY DIFFRACTION93.94
1.99-2.050.33451280.28512633X-RAY DIFFRACTION96
2.05-2.110.29661420.26122680X-RAY DIFFRACTION97.04
2.11-2.170.35971810.26442594X-RAY DIFFRACTION95.82
2.17-2.250.49241580.37912484X-RAY DIFFRACTION90.7
2.25-2.340.31451350.29082368X-RAY DIFFRACTION85.48
2.34-2.450.26661340.24632696X-RAY DIFFRACTION96.88
2.45-2.580.32461320.24172674X-RAY DIFFRACTION96.79
2.58-2.740.351280.23632723X-RAY DIFFRACTION97.74
2.74-2.950.31320.25812732X-RAY DIFFRACTION97.81
2.95-3.250.25951290.24992715X-RAY DIFFRACTION97.7
3.25-3.720.28011460.22182631X-RAY DIFFRACTION94.88
3.72-4.690.24141400.18122711X-RAY DIFFRACTION96.45
4.69-690.24091470.19232804X-RAY DIFFRACTION98.17

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