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- PDB-5xkx: Crystal structure of WT DddY -

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Basic information

Entry
Database: PDB / ID: 5xkx
TitleCrystal structure of WT DddY
ComponentsUncharacterized protein
KeywordsLYASE / Dimethylsulfoniopropionate (DMSP) lyase
Function / homology: / Dimethlysulfonioproprionate lyase / Dimethlysulfonioproprionate lyase / dimethylpropiothetin dethiomethylase activity / RmlC-like jelly roll fold / metal ion binding / ACETATE ION / Uncharacterized protein
Function and homology information
Biological speciesAcinetobacter bereziniae NIPH 3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsLi, C.Y. / Zhang, Y.Z.
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Mechanistic Insights into Dimethylsulfoniopropionate Lyase DddY, a New Member of the Cupin Superfamily.
Authors: Li, C.Y. / Zhang, D. / Chen, X.L. / Wang, P. / Shi, W.L. / Li, P.Y. / Zhang, X.Y. / Qin, Q.L. / Todd, J.D. / Zhang, Y.Z.
History
DepositionMay 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9723
Polymers46,8481
Non-polymers1242
Water10,106561
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area70 Å2
ΔGint-27 kcal/mol
Surface area15660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.063, 72.070, 88.046
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized protein / DMSP lyase


Mass: 46847.676 Da / Num. of mol.: 1
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) / Strain (production host): BL21(DE3) / References: UniProt: N8X9V6
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M ammonium acetate, 0.1 M Bis-Tris (pH 6.5) and 25% (wt/vol) polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: CCD / Date: Sep 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 59702 / % possible obs: 93.5 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 27.8
Reflection shellResolution: 1.5→1.55 Å / % possible obs: 97.4 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 7 / Rsym value: 0.3

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→44.023 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.51
RfactorNum. reflection% reflection
Rfree0.1842 3016 5.06 %
Rwork0.1328 --
obs0.1354 59635 93.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→44.023 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3074 0 5 561 3640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053212
X-RAY DIFFRACTIONf_angle_d0.7924371
X-RAY DIFFRACTIONf_dihedral_angle_d17.1541197
X-RAY DIFFRACTIONf_chiral_restr0.077459
X-RAY DIFFRACTIONf_plane_restr0.005566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4905-1.51380.22321130.14462392X-RAY DIFFRACTION88
1.5138-1.53860.22131420.1412681X-RAY DIFFRACTION97
1.5386-1.56520.21411430.13612609X-RAY DIFFRACTION96
1.5652-1.59360.17581540.13442626X-RAY DIFFRACTION97
1.5936-1.62430.19711510.13342634X-RAY DIFFRACTION97
1.6243-1.65740.19271260.13292653X-RAY DIFFRACTION96
1.6574-1.69350.20281450.13452631X-RAY DIFFRACTION96
1.6935-1.73290.20561330.13482590X-RAY DIFFRACTION96
1.7329-1.77620.22421420.12682624X-RAY DIFFRACTION96
1.7762-1.82420.20521150.12972615X-RAY DIFFRACTION95
1.8242-1.87790.17281350.1382593X-RAY DIFFRACTION94
1.8779-1.93850.19641290.13432618X-RAY DIFFRACTION94
1.9385-2.00780.19111390.1312605X-RAY DIFFRACTION94
2.0078-2.08820.18631400.13492564X-RAY DIFFRACTION93
2.0882-2.18320.17441430.12642557X-RAY DIFFRACTION93
2.1832-2.29830.1681310.12852528X-RAY DIFFRACTION92
2.2983-2.44230.18131540.13162542X-RAY DIFFRACTION92
2.4423-2.63090.20881310.13382545X-RAY DIFFRACTION91
2.6309-2.89560.16221390.13392540X-RAY DIFFRACTION91
2.8956-3.31450.16881240.13692494X-RAY DIFFRACTION89
3.3145-4.17540.15871510.12612472X-RAY DIFFRACTION87
4.1754-44.04220.20611360.13682506X-RAY DIFFRACTION84

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