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Basic information

Entry
Database: PDB / ID: 5jsp
TitleNew Mechanistic Insight from Substrate and Product Bound Structures of the Metal-dependent Dimethylsulfoniopropionate Lyase DddQ
ComponentsDimethlysulfonioproprionate lyase DddQ
KeywordsLYASE / dimethylsulfoniopropionate / cupin / metalloenzyme
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
BROMIDE ION / 3-(dimethyl-lambda~4~-sulfanyl)propanoic acid / : / Dimethylsulfoniopropionate lyase DddQ
Similarity search - Component
Biological speciesRuegeria lacuscaerulensis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBrummett, A.E. / Dey, M.
Funding support United States, 1items
OrganizationGrant numberCountry
University of Iowa, College of Liberal Arts and Sciences United States
CitationJournal: Biochemistry / Year: 2016
Title: New Mechanistic Insight from Substrate- and Product-Bound Structures of the Metal-Dependent Dimethylsulfoniopropionate Lyase DddQ.
Authors: Brummett, A.E. / Dey, M.
History
DepositionMay 9, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Derived calculations
Revision 1.2Feb 13, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Sep 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 / 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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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

Downloads & links

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Assembly

Deposited unit
A: Dimethlysulfonioproprionate lyase DddQ
B: Dimethlysulfonioproprionate lyase DddQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,63915
Polymers44,7902
Non-polymers84913
Water5,296294
1
A: Dimethlysulfonioproprionate lyase DddQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8658
Polymers22,3951
Non-polymers4707
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dimethlysulfonioproprionate lyase DddQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7737
Polymers22,3951
Non-polymers3786
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.745, 88.101, 92.998
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Dimethlysulfonioproprionate lyase DddQ / DMSP lyase


Mass: 22395.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruegeria lacuscaerulensis (strain DSM 11314 / KCTC 2953 / ITI-1157) (bacteria)
Strain: DSM 11314 / KCTC 2953 / ITI-1157 / Gene: dddQ, SL1157_0332 / Production host: Escherichia coli (E. coli)
References: UniProt: D0CY60, dimethylpropiothetin dethiomethylase

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Non-polymers , 6 types, 307 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-DQY / 3-(dimethyl-lambda~4~-sulfanyl)propanoic acid


Mass: 136.213 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O2S
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 2.23 Å3/Da / Density % sol: 44.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris propane pH 6.5, 0.2 M NaBr, 21% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979332 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979332 Å / Relative weight: 1
ReflectionResolution: 2.2→38.769 Å / Num. all: 20992 / Num. obs: 20992 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 16.94 Å2 / Rpim(I) all: 0.036 / Rrim(I) all: 0.096 / Rsym value: 0.082 / Net I/av σ(I): 8.47 / Net I/σ(I): 17 / Num. measured all: 150584
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.327.20.26332181130090.1140.3080.2637.199.8
2.32-2.467.30.2173.62087128490.0920.2520.2178.199.9
2.46-2.637.30.1714.51959726790.0730.1990.17110.1100
2.63-2.847.30.1325.91829925140.0570.1550.13212.7100
2.84-3.117.30.0918.31687523230.0390.1060.09117.2100
3.11-3.487.20.06411.41529321270.0280.0750.06422.3100
3.48-4.027.10.04813.51328118710.0210.0560.04827.899.9
4.02-4.9270.03616.21135016110.0160.0430.03632.399.9
4.92-6.966.90.04413.7874412720.020.0520.04429100
6.96-38.7696.10.03614.844637370.0170.0430.03633.598.3

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.2data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LA2

4la2


Resolution: 2.2→38.769 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2278 1005 4.81 %4.8%
Rwork0.1898 19890 --
obs0.1916 20895 99.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 52.27 Å2 / Biso mean: 16.1374 Å2 / Biso min: 4.35 Å2
Refinement stepCycle: final / Resolution: 2.2→38.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2942 0 32 294 3268
Biso mean--27.18 22.27 -
Num. residues----381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163073
X-RAY DIFFRACTIONf_angle_d0.9144201
X-RAY DIFFRACTIONf_chiral_restr0.057437
X-RAY DIFFRACTIONf_plane_restr0.006542
X-RAY DIFFRACTIONf_dihedral_angle_d18.4161055
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.3160.24941290.22282802293199
2.316-2.46110.27081490.201627812930100
2.4611-2.65110.28241380.20627832921100
2.6511-2.91780.22911510.200628362987100
2.9178-3.33980.23511330.186928462979100
3.3398-4.2070.20011460.166328663012100
4.207-38.77490.1991590.18412976313599

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