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- PDB-5tg0: Crystal structure of the dimethylsulfoniopropionate (DMSP) lyase ... -

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Basic information

Entry
Database: PDB / ID: 5tg0
TitleCrystal structure of the dimethylsulfoniopropionate (DMSP) lyase DddK complexed with iron and zinc
Componentsdimethylsulfoniopropionate lyase DddK
KeywordsLYASE / DMSP lyase / Cupin / Nickel dependent / Metal binding
Function / homologyCupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / outer membrane-bounded periplasmic space / metal ion binding / : / Novel protein with potential Cupin domain
Function and homology information
Biological speciesPelagibacter ubique (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.44 Å
AuthorsSchnicker, N.J. / Dey, M.
Funding support United States, 1items
OrganizationGrant numberCountry
University of Iowa College of Liberal Arts and Sciences United States
CitationJournal: Biochemistry / Year: 2017
Title: Structural and Biochemical Insights into Dimethylsulfoniopropionate Cleavage by Cofactor-Bound DddK from the Prolific Marine Bacterium Pelagibacter.
Authors: Schnicker, N.J. / De Silva, S.M. / Todd, J.D. / Dey, M.
History
DepositionSep 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: dimethylsulfoniopropionate lyase DddK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7333
Polymers16,6121
Non-polymers1212
Water3,027168
1
A: dimethylsulfoniopropionate lyase DddK
hetero molecules

A: dimethylsulfoniopropionate lyase DddK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4666
Polymers33,2232
Non-polymers2434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area3660 Å2
ΔGint-134 kcal/mol
Surface area13120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.065, 85.416, 54.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-454-

HOH

21A-460-

HOH

31A-468-

HOH

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Components

#1: Protein dimethylsulfoniopropionate lyase DddK


Mass: 16611.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Residues 1-20 in the sequence are from the vector for the His tag.
Source: (gene. exp.) Pelagibacter ubique (strain HTCC1062) (bacteria)
Strain: HTCC1062 / Gene: SAR11_0394 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4FNM4
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 1.92 Å3/Da / Density % sol: 36.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, 0.2 M NaCl, 20% PEG 3000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.44→46.28 Å / Num. obs: 23496 / % possible obs: 99.6 % / Redundancy: 6 % / Biso Wilson estimate: 12.65 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.015 / Rrim(I) all: 0.037 / Net I/σ(I): 29.8 / Num. measured all: 140675
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.44-1.524.30.1690.971197.6
4.55-46.285.80.0250.999199.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHASERphasing
PHENIX1.10_2155refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.44→27.532 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12
RfactorNum. reflection% reflection
Rfree0.1399 2243 5.06 %
Rwork0.1101 --
obs0.1116 44346 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 61.74 Å2 / Biso mean: 18.1367 Å2 / Biso min: 6.01 Å2
Refinement stepCycle: final / Resolution: 1.44→27.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1060 0 2 172 1234
Biso mean--9.79 31.02 -
Num. residues----137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011203
X-RAY DIFFRACTIONf_angle_d1.1051652
X-RAY DIFFRACTIONf_chiral_restr0.096176
X-RAY DIFFRACTIONf_plane_restr0.007217
X-RAY DIFFRACTIONf_dihedral_angle_d12.108439
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.44-1.47130.20731190.152237235684
1.4713-1.50550.17081500.114626452795100
1.5055-1.54320.17661340.095827092843100
1.5432-1.58490.1751170.099326902807100
1.5849-1.63150.12821340.100426442778100
1.6315-1.68420.13971450.094826542799100
1.6842-1.74440.15651570.098726502807100
1.7444-1.81420.15831370.098226882825100
1.8142-1.89680.14371360.098426482784100
1.8968-1.99670.09441580.097326412799100
1.9967-2.12180.12881200.096426662786100
2.1218-2.28550.12561410.095126552796100
2.2855-2.51540.15841370.110926502787100
2.5154-2.87910.14511490.11992652280199
2.8791-3.6260.14111560.11832635279199
3.626-27.53750.13381530.12592639279299

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