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- PDB-5y4k: Crystal structure of DddY mutant Y260A -

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Basic information

Entry
Database: PDB / ID: 5y4k
TitleCrystal structure of DddY mutant Y260A
ComponentsDMSP lyase DddY
KeywordsLYASE / DMSP lyase
Function / homologyDimethlysulfonioproprionate lyase / Dimethlysulfonioproprionate lyase / dimethylpropiothetin dethiomethylase activity / RmlC-like jelly roll fold / metal ion binding / ACRYLIC ACID / Uncharacterized protein
Function and homology information
Biological speciesAcinetobacter bereziniae NIPH 3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, Y.Z. / Li, C.Y.
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
DepositionAug 3, 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 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: DMSP lyase DddY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8933
Polymers46,7561
Non-polymers1372
Water7,891438
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15740 Å2
Unit cell
Length a, b, c (Å)60.841, 72.646, 89.547
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 DMSP lyase DddY / Uncharacterized protein


Mass: 46755.582 Da / Num. of mol.: 1 / Mutation: Y260A
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-AKR / ACRYLIC ACID


Mass: 72.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H2O

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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: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris-HCl (pH 8.5) and 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9789 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 27489 / % possible obs: 100 % / Redundancy: 24.9 % / Rmerge(I) obs: 0.167 / Net I/σ(I): 41.6
Reflection shellResolution: 2→2.03 Å / Redundancy: 23.2 % / Mean I/σ(I) obs: 18 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XKX

5xkx


Resolution: 2→30.42 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 16.9
RfactorNum. reflection% reflection
Rfree0.1878 1380 5.04 %
Rwork0.1439 --
obs0.1461 27359 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→30.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3067 0 6 438 3511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073168
X-RAY DIFFRACTIONf_angle_d0.7944306
X-RAY DIFFRACTIONf_dihedral_angle_d14.5991897
X-RAY DIFFRACTIONf_chiral_restr0.05454
X-RAY DIFFRACTIONf_plane_restr0.006556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.07140.20441480.13622510X-RAY DIFFRACTION98
2.0714-2.15440.19651340.13812569X-RAY DIFFRACTION100
2.1544-2.25240.20671400.13842585X-RAY DIFFRACTION100
2.2524-2.37110.20431270.14472560X-RAY DIFFRACTION100
2.3711-2.51960.21971170.15352602X-RAY DIFFRACTION100
2.5196-2.7140.2051520.14862584X-RAY DIFFRACTION100
2.714-2.98690.17641400.1492582X-RAY DIFFRACTION100
2.9869-3.41860.1831680.1512597X-RAY DIFFRACTION100
3.4186-4.30520.16591310.1322654X-RAY DIFFRACTION100
4.3052-30.4240.17881230.14792736X-RAY DIFFRACTION98

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