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

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Basic information

Entry
Database: PDB / ID: 5tfz
TitleCrystal structure of the dimethylsulfoniopropionate (DMSP) lyase DddK complexed with nickel and diacrylate
Componentsdimethylsulfoniopropionate lyase DddK
KeywordsOXIDOREDUCTASE / DMSP lyase / Cupin / Nickel dependent / Metal binding
Function / homology
Function and homology information


outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
3-(acryloyloxy)propanoic acid / NICKEL (II) ION / DI(HYDROXYETHYL)ETHER / Novel protein with potential Cupin domain
Similarity search - Component
Biological speciesPelagibacter ubique (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 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.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

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Assembly

Deposited unit
A: dimethylsulfoniopropionate lyase DddK
B: dimethylsulfoniopropionate lyase DddK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9479
Polymers33,2232
Non-polymers7247
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-23 kcal/mol
Surface area10860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.352, 54.667, 118.335
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 dimethylsulfoniopropionate lyase DddK


Mass: 16611.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residues 1-20 in the sequence are from the vector for a 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-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-7BC / 3-(acryloyloxy)propanoic acid


Mass: 144.125 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / 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: 2.11 Å3/Da / Density % sol: 41.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Potassium thiocyanate, 30% PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Sep 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→59.17 Å / Num. obs: 14946 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 23.92 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.4
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.617 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
Aimless0.5.27data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→59.17 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.99
RfactorNum. reflection% reflection
Rfree0.224 1371 4.99 %
Rwork0.172 --
obs0.175 27455 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.33 Å2
Refinement stepCycle: LAST / Resolution: 2.2→59.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1992 0 43 137 2172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112085
X-RAY DIFFRACTIONf_angle_d1.0812821
X-RAY DIFFRACTIONf_dihedral_angle_d13.9291188
X-RAY DIFFRACTIONf_chiral_restr0.063299
X-RAY DIFFRACTIONf_plane_restr0.006363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.27880.28451480.21772584X-RAY DIFFRACTION98
2.2788-2.370.23541230.20482619X-RAY DIFFRACTION100
2.37-2.47790.2986960.20262630X-RAY DIFFRACTION100
2.4779-2.60850.2782980.19322666X-RAY DIFFRACTION100
2.6085-2.7720.19991600.18132588X-RAY DIFFRACTION100
2.772-2.9860.24021490.18032577X-RAY DIFFRACTION100
2.986-3.28640.21431580.16622622X-RAY DIFFRACTION100
3.2864-3.76190.20251330.15012586X-RAY DIFFRACTION100
3.7619-4.73930.19941550.142611X-RAY DIFFRACTION100
4.7393-59.18890.22631510.17942601X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7118-0.38160.41320.2965-0.1170.51440.065-0.1262-0.0779-0.2226-0.00570.12330.1134-0.02190.08580.1571-0.01620.0330.2035-0.00820.2137-0.435-25.56023.0223
20.51330.0575-0.47930.9479-0.08770.964-0.08120.0938-0.1185-0.11760.1065-0.01870.3315-0.06410.03230.1818-0.0133-0.01520.14250.01950.1591-8.4819-27.457813.6878
32.8551.6744-0.06721.21360.57921.67940.0747-0.6098-0.5308-0.0497-0.3741-0.61860.43470.2299-0.07290.22430.05880.0160.2520.03440.35693.5685-32.084816.6248
40.3005-0.2113-0.04341.40840.34510.08540.1348-0.1061-0.12150.3777-0.13120.3762-0.03390.14220.01860.15460.04170.04480.22150.03350.2104-12.9796-21.209525.6896
50.25040.23120.10330.33890.34180.54280.0199-0.16630.06820.2586-0.07580.1294-0.2278-0.0228-0.00050.22030.00430.00080.1988-0.01350.1876-8.7838-7.221521.8347
60.19690.1354-0.21830.0831-0.1550.44190.029-0.1212-0.01190.0205-0.030.0389-0.06660.0973-0.00120.21630.0035-0.00980.1241-0.02780.1952-0.4835-5.267713.0646
70.11040.1471-0.18290.3214-0.17970.2959-0.0370.08040.0355-0.1939-0.06060.1134-0.03410.10170.00030.1426-0.0091-0.01320.1757-0.00830.14761.9675-6.10736.5576
80.19990.07850.18060.19870.06280.138-0.1622-0.25780.05260.22550.17870.0606-0.2198-0.1684-0.00450.19420.011-0.03660.15860.02050.2307-7.8431-6.273410.4415
90.14450.00240.03860.11570.11150.10470.2265-0.1262-0.03220.3092-0.1984-0.213-0.07440.2406-0.0010.2712-0.0107-0.03610.2473-0.02370.20684.0337-7.400224.0854
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 0 THROUGH 30 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 31 THROUGH 112 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 113 THROUGH 126 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID -4 THROUGH 10 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 11 THROUGH 47 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 48 THROUGH 68 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 69 THROUGH 99 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 100 THROUGH 112 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 113 THROUGH 126 )

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