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- PDB-8hlf: Crystal structure of DddK-DMSOP complex -

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Basic information

Entry
Database: PDB / ID: 8hlf
TitleCrystal structure of DddK-DMSOP complex
ComponentsNovel protein with potential Cupin domain
KeywordsLYASE / DMSOP lyase / complex
Function / homology: / Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / metal ion binding / Chem-LNI / : / Novel protein with potential Cupin domain
Function and homology information
Biological speciesCandidatus Pelagibacter ubique HTCC1062 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Novel protein with potential Cupin domain
B: Novel protein with potential Cupin domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7666
Polymers30,3542
Non-polymers4124
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-26 kcal/mol
Surface area11400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.807, 92.804, 38.808
Angle α, β, γ (deg.)90.00, 117.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Novel protein with potential Cupin domain


Mass: 15177.058 Da / Num. of mol.: 2 / Mutation: Y64A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Pelagibacter ubique HTCC1062 (bacteria)
Gene: SAR11_0394 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4FNM4
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mn
#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.: 275 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: SPG buffer, PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 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: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.62→26.66 Å / Num. obs: 28768 / % possible obs: 98.35 % / Redundancy: 3.4 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.036 / Rrim(I) all: 0.067 / Net I/σ(I): 22.5
Reflection shellResolution: 1.62→1.678 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 6.4 / Num. unique obs: 2802 / CC1/2: 0.947 / CC star: 0.986 / Rpim(I) all: 0.121 / Rrim(I) all: 0.227

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A53

6a53


Resolution: 1.62→26.66 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.199 1448 5.03 %
Rwork0.165 --
obs0.167 28768 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.62→26.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1974 0 20 275 2269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062042
X-RAY DIFFRACTIONf_angle_d0.9112764
X-RAY DIFFRACTIONf_dihedral_angle_d18.9291180
X-RAY DIFFRACTIONf_chiral_restr0.06294
X-RAY DIFFRACTIONf_plane_restr0.005350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.67790.24371360.18992672X-RAY DIFFRACTION96
1.6779-1.74510.22241470.17482680X-RAY DIFFRACTION97
1.7451-1.82450.1981470.18022707X-RAY DIFFRACTION98
1.8245-1.92070.22821600.17622707X-RAY DIFFRACTION98
1.9207-2.0410.21411750.16912717X-RAY DIFFRACTION98
2.041-2.19850.20551570.16682701X-RAY DIFFRACTION99
2.1985-2.41960.21361230.16982773X-RAY DIFFRACTION99
2.4196-2.76940.21661540.16962736X-RAY DIFFRACTION99
2.7694-3.48790.17861210.16412795X-RAY DIFFRACTION99
3.4879-26.6590.16561280.14832832X-RAY DIFFRACTION100

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