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Basic information

Entry
Database: PDB / ID: 5jsr
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
ACRYLIC ACID / BROMIDE ION / : / Dimethylsulfonioproprionate lyase DddQ
Similarity search - Component
Biological speciesRuegeria lacuscaerulensis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.2Sep 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)45,38313
Polymers44,7902
Non-polymers59311
Water3,225179
1
A: Dimethlysulfonioproprionate lyase DddQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7097
Polymers22,3951
Non-polymers3146
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dimethlysulfonioproprionate lyase DddQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6746
Polymers22,3951
Non-polymers2795
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.724, 88.170, 93.082
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 , 5 types, 190 molecules

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


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-AKR / ACRYLIC ACID / Acrylic acid


Mass: 72.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O2
#4: Chemical ChemComp-BR / BROMIDE ION / Bromide


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


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 44.89 %
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, 23% 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: 2.5→38.77 Å / Num. all: 14485 / Num. obs: 14485 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 19.18 Å2 / Rpim(I) all: 0.042 / Rrim(I) all: 0.113 / Rsym value: 0.097 / Net I/av σ(I): 7.76 / Net I/σ(I): 15.3 / Num. measured all: 103679
Reflection shell

Diffraction-ID: 1 / Rejects: 0

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
2.5-2.647.30.3012.61522520760.1280.3490.3015.9100
2.64-2.87.30.2433.21439319650.1030.2820.2437.4100
2.8-2.997.30.1814.41350018490.0770.2110.1819.6100
2.99-3.237.30.1361257617280.0550.1510.1312.7100
3.23-3.547.20.098.61159816010.0380.1040.0917100
3.54-3.957.20.06711.11037214450.0290.0780.06721.4100
3.95-4.567.10.04914.4928113100.0210.0570.04926.7100
4.56-5.5970.04914775611100.0210.0570.04924100
5.59-7.916.80.05812.959818850.0260.0680.05822.899.9
7.91-38.775.80.03714.229975160.0190.0460.03728.998.4

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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: 2.5→33.655 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2474 691 4.8 %4.8%
Rwork0.211 13708 --
obs0.2128 14399 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 47.86 Å2 / Biso mean: 19.6369 Å2 / Biso min: 6.16 Å2
Refinement stepCycle: final / Resolution: 2.5→33.655 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2926 0 19 179 3124
Biso mean--29.14 24.61 -
Num. residues----380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143038
X-RAY DIFFRACTIONf_angle_d0.5724156
X-RAY DIFFRACTIONf_chiral_restr0.043434
X-RAY DIFFRACTIONf_plane_restr0.004538
X-RAY DIFFRACTIONf_dihedral_angle_d18.9161031
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.6930.27551120.23427142826100
2.693-2.96380.29821310.221726952826100
2.9638-3.39230.20711350.205527192854100
3.3923-4.27260.25631630.18927292892100
4.2726-33.65780.23411500.22122851300199

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