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- PDB-5cu1: Crystal structure of DMSP lyase DddQ from Ruegeria pomeroyi DSS-3 -

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Basic information

Entry
Database: PDB / ID: 5cu1
TitleCrystal structure of DMSP lyase DddQ from Ruegeria pomeroyi DSS-3
ComponentsDMSP lyase
KeywordsLYASE / Metalloenzyme / DMSP / Cupin
Function / homology
Function and homology information


dimethylpropiothetin dethiomethylase / dimethylpropiothetin dethiomethylase activity / metal ion binding
Similarity search - Function
Dimethlysulfonioproprionate lyase / Dimethlysulfonioproprionate lyase / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Dimethylsulfonioproprionate lyase DddQ
Similarity search - Component
Biological speciesRuegeria pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChong, S.Y. / Moran, M.A. / Lanzilotta, W.N. / Whitman, W.B.
CitationJournal: To Be Published
Title: To be Published
Authors: Chong, S.Y. / Lanzilotta, W.N.
History
DepositionJul 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DMSP lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4162
Polymers23,3601
Non-polymers561
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.582, 69.878, 49.731
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DMSP lyase


Mass: 23360.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3) (bacteria)
Strain: ATCC 700808 / DSM 15171 / DSS-3 / Gene: dddQ, SPO1596 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5LT18
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M ammonium acetate, 0.1M bis-tris pH 5.5, 17% w/v PEG 10,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 15, 2014
RadiationMonochromator: SI 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→46.62 Å / Num. obs: 10150 / % possible obs: 99.9 % / Redundancy: 5.9 % / Rsym value: 1.071 / Net I/σ(I): 9.69
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.95 / % possible all: 93.7

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
CootX11-2.7.7model building
HKL-2000data scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LA2

4la2


Resolution: 2.3→46.619 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2674 479 4.72 %
Rwork0.2163 --
obs0.2189 10150 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→46.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1527 0 1 62 1590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081581
X-RAY DIFFRACTIONf_angle_d1.1192167
X-RAY DIFFRACTIONf_dihedral_angle_d14.629561
X-RAY DIFFRACTIONf_chiral_restr0.042228
X-RAY DIFFRACTIONf_plane_restr0.008290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3002-2.6330.32931470.26473154X-RAY DIFFRACTION100
2.633-3.31720.31571660.24273189X-RAY DIFFRACTION100
3.3172-46.62850.22031660.18573328X-RAY DIFFRACTION100

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