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- PDB-8hle: Structure of DddY-DMSOP complex -

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Basic information

Entry
Database: PDB / ID: 8hle
TitleStructure of DddY-DMSOP complex
ComponentsDMSP lyase DddY
KeywordsLYASE / DMSOP lyase / complex
Function / homology: / Dimethlysulfonioproprionate lyase / Dimethlysulfonioproprionate lyase / dimethylpropiothetin dethiomethylase activity / RmlC-like jelly roll fold / metal ion binding / Chem-LNI / Uncharacterized protein
Function and homology information
Biological speciesAcinetobacter bereziniae NIPH 3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsPeng, M. / Li, C.Y. / Zhang, Y.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Microbiol / Year: 2023
Title: DMSOP-cleaving enzymes are diverse and widely distributed in marine microorganisms.
Authors: Carrion, O. / Li, C.Y. / Peng, M. / Wang, J. / Pohnert, G. / Azizah, M. / Zhu, X.Y. / Curson, A.R.J. / Wang, Q. / Walsham, K.S. / Zhang, X.H. / Monaco, S. / Harvey, J.M. / Chen, X.L. / Gao, ...Authors: Carrion, O. / Li, C.Y. / Peng, M. / Wang, J. / Pohnert, G. / Azizah, M. / Zhu, X.Y. / Curson, A.R.J. / Wang, Q. / Walsham, K.S. / Zhang, X.H. / Monaco, S. / Harvey, J.M. / Chen, X.L. / Gao, C. / Wang, N. / Wang, X.J. / Wang, P. / Giovanonni, S.J. / Lee, C.P. / Suffridge, C.P. / Zhang, Y. / Luo, Z. / Wang, D. / Todd, J.D. / Zhang, Y.Z.
History
DepositionNov 30, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _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 / _citation.year
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DMSP lyase DddY
B: DMSP lyase DddY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9446
Polymers93,5112
Non-polymers4334
Water20,7171150
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-2 kcal/mol
Surface area30740 Å2
Unit cell
Length a, b, c (Å)65.803, 73.387, 87.368
Angle α, β, γ (deg.)90.00, 91.14, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DMSP lyase DddY / Uncharacterized protein


Mass: 46755.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter bereziniae NIPH 3 (bacteria)
Gene: F963_02809 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: N8X9V6
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-LNI / 3-[dimethyl(oxidanyl)-$l^{4}-sulfanyl]propanoic acid / Dimethylsulfoxonium propionate


Mass: 151.204 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C5H11O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1150 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, TRIS-HCL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.91→36.724 Å / Num. obs: 62913 / % possible obs: 97.2 % / Redundancy: 6.6 % / CC1/2: 0.981 / CC star: 0.995 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.051 / Rrim(I) all: 0.134 / Net I/σ(I): 23.3
Reflection shellResolution: 1.91→1.978 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 7.65 / Num. unique obs: 5683 / CC1/2: 0.888 / CC star: 0.97 / Rpim(I) all: 0.149 / Rrim(I) all: 0.389 / % possible all: 88.19

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XKX

5xkx


Resolution: 1.91→36.724 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.201 3193 5.08 %
Rwork0.1597 --
obs0.1618 62858 97.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.91→36.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6132 0 20 1150 7302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066318
X-RAY DIFFRACTIONf_angle_d0.818580
X-RAY DIFFRACTIONf_dihedral_angle_d3.9295260
X-RAY DIFFRACTIONf_chiral_restr0.051904
X-RAY DIFFRACTIONf_plane_restr0.0051106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.93840.24941080.19162087X-RAY DIFFRACTION77
1.9384-1.96860.24591460.18852543X-RAY DIFFRACTION97
1.9686-2.00090.26491380.18042562X-RAY DIFFRACTION97
2.0009-2.03540.19931430.16972590X-RAY DIFFRACTION97
2.0354-2.07240.24731290.17412581X-RAY DIFFRACTION98
2.0724-2.11230.23761280.17662615X-RAY DIFFRACTION98
2.1123-2.15540.2221620.17782526X-RAY DIFFRACTION97
2.1554-2.20230.23731350.17232597X-RAY DIFFRACTION98
2.2023-2.25350.23591490.17022578X-RAY DIFFRACTION97
2.2535-2.30980.24911260.16862599X-RAY DIFFRACTION98
2.3098-2.37230.23871360.16732611X-RAY DIFFRACTION98
2.3723-2.44210.19241560.16092615X-RAY DIFFRACTION98
2.4421-2.52090.21711480.16662614X-RAY DIFFRACTION98
2.5209-2.61090.22471210.16272610X-RAY DIFFRACTION98
2.6109-2.71550.21381330.17522641X-RAY DIFFRACTION98
2.7155-2.8390.21871380.16022633X-RAY DIFFRACTION99
2.839-2.98860.20491350.17212640X-RAY DIFFRACTION99
2.9886-3.17580.20311470.16362643X-RAY DIFFRACTION99
3.1758-3.42080.18781470.15232639X-RAY DIFFRACTION99
3.4208-3.76470.17971430.14022663X-RAY DIFFRACTION99
3.7647-4.30880.15331420.13312668X-RAY DIFFRACTION99
4.3088-5.42580.14951400.1312696X-RAY DIFFRACTION99
5.4258-36.7240.17621430.16662714X-RAY DIFFRACTION98

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