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- PDB-4la2: Crystal structure of dimethylsulphoniopropionate (DMSP) lyase DddQ -

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Basic information

Entry
Database: PDB / ID: 4la2
TitleCrystal structure of dimethylsulphoniopropionate (DMSP) lyase DddQ
ComponentsDimethylsulphoniopropionate (DMSP) lyase DddQ
KeywordsLYASE / Cupin motif / DMSP lyase
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 speciesSilicibacter lacuscaerulensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsZhang, Y. / Li, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Molecular insight into bacterial cleavage of oceanic dimethylsulfoniopropionate into dimethyl sulfide
Authors: Li, C. / Wei, T. / Zhang, S. / Chen, X. / Gao, X. / Wang, P. / Xie, B. / Su, H. / Qin, Q. / Zhang, X. / Yu, J. / Zhang, H. / Zhou, B. / Yang, G. / Zhang, Y.
History
DepositionJun 19, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dimethylsulphoniopropionate (DMSP) lyase DddQ
B: Dimethylsulphoniopropionate (DMSP) lyase DddQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5646
Polymers44,0432
Non-polymers5214
Water7,855436
1
A: Dimethylsulphoniopropionate (DMSP) lyase DddQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2823
Polymers22,0221
Non-polymers2612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dimethylsulphoniopropionate (DMSP) lyase DddQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2823
Polymers22,0221
Non-polymers2612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.383, 85.303, 87.457
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 Dimethylsulphoniopropionate (DMSP) lyase DddQ


Mass: 22021.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter lacuscaerulensis (bacteria)
Strain: ITI-1157 / Gene: SL1157_0332 / Production host: Escherichia coli (E. coli) / References: UniProt: D0CY60
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.05 Å3/Da / Density % sol: 39.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M sodium chloride, 0.1M MES, 20% (w/v) PEG 2000 MME , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 48408 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 18.38 Å2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.6-1.66199.2
3.45-50199.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
MLPHAREphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→42.336 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8018 / SU ML: 0.18 / σ(F): 1.34 / Phase error: 25.81 / Stereochemistry target values: Overall
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2444 5.07 %RANDOM
Rwork0.1968 ---
all0.197 48250 --
obs0.1978 48408 99.36 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.508 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso max: 67.88 Å2 / Biso mean: 22.3996 Å2 / Biso min: 9.41 Å2
Baniso -1Baniso -2Baniso -3
1--6.9611 Å2-0 Å20 Å2
2--7.8926 Å20 Å2
3----0.9315 Å2
Refinement stepCycle: LAST / Resolution: 1.6→42.336 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2990 0 26 436 3452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073148
X-RAY DIFFRACTIONf_angle_d1.0954303
X-RAY DIFFRACTIONf_dihedral_angle_d16.0761101
X-RAY DIFFRACTIONf_chiral_restr0.074449
X-RAY DIFFRACTIONf_plane_restr0.006559
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5997-1.63240.31571480.25072575272397
1.6324-1.66790.27451530.23572636278999
1.6679-1.70670.30641230.21912665278899
1.7067-1.74930.27131360.21292675281199
1.7493-1.79660.24231490.21362645279499
1.7966-1.84950.25381460.199326782824100
1.8495-1.90920.23291320.196426582790100
1.9092-1.97740.21171430.187826732816100
1.9774-2.05660.23291340.191726902824100
2.0566-2.15020.2251550.19126842839100
2.1502-2.26360.26861380.187527082846100
2.2636-2.40540.21271550.1926772832100
2.4054-2.59110.21691410.194327392880100
2.5911-2.85180.21911370.207827312868100
2.8518-3.26430.22661310.200427482879100
3.2643-4.11210.18141590.180427542913100
4.1121-42.35110.18131640.19862870303499
Refinement TLS params.Method: refined / Origin x: 24.1355 Å / Origin y: -11.5787 Å / Origin z: -20.5768 Å
111213212223313233
T0.1112 Å20.0007 Å2-0.0058 Å2-0.0928 Å20.0038 Å2--0.1131 Å2
L0.2114 °20.0268 °2-0.0682 °2-0.0151 °20.0048 °2--0.2811 °2
S-0.0005 Å °0.0145 Å °0.0054 Å °-0.0035 Å °-0.008 Å °0.0038 Å °0.0263 Å °-0.0165 Å °0.0054 Å °
Refinement TLS groupSelection details: all

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