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- PDB-7wdw: DsyB in complex with SAH and MTHB -

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Basic information

Entry
Database: PDB / ID: 7wdw
TitleDsyB in complex with SAH and MTHB
ComponentsDSYB
KeywordsTRANSFERASE / Complex / SAM-dependent methyltransferase
Function / homology4-methylsulfanyl-2-oxidanyl-butanoic acid / S-ADENOSYL-L-HOMOCYSTEINE
Function and homology information
Biological speciesNisaea denitrificans DSM 18348 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsLi, C.Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mlife / Year: 2022
Title: Mechanistic insights into the key marine dimethylsulfoniopropionate synthesis enzyme DsyB/DSYB.
Authors: Li, C.Y. / Crack, J.C. / Newton-Payne, S. / Murphy, A.R.J. / Chen, X.L. / Pinchbeck, B.J. / Zhou, S. / Williams, B.T. / Peng, M. / Zhang, X.H. / Chen, Y.
History
DepositionDec 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DSYB
B: DSYB
C: DSYB
D: DSYB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,68616
Polymers148,0594
Non-polymers2,62712
Water5,152286
1
A: DSYB
D: DSYB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3438
Polymers74,0302
Non-polymers1,3136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7870 Å2
ΔGint-57 kcal/mol
Surface area24290 Å2
MethodPISA
2
B: DSYB
C: DSYB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,3438
Polymers74,0302
Non-polymers1,3136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7670 Å2
ΔGint-53 kcal/mol
Surface area24810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.103, 69.292, 104.340
Angle α, β, γ (deg.)90.000, 92.190, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DSYB


Mass: 37014.828 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nisaea denitrificans DSM 18348 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-H9L / 4-methylsulfanyl-2-oxidanyl-butanoic acid


Mass: 150.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H10O3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2 M NaCl, 0.1 M Tris (pH 8.0) and 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 49532 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 32.77 Å2 / Rmerge(I) obs: 0.094 / Χ2: 2.542 / Net I/σ(I): 11.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.457 / Num. unique obs: 5100 / Χ2: 3.175 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DFD

7dfd
PDB Unreleased entry


Resolution: 2.39→37.16 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 30 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.268 2325 5.06 %
Rwork0.187 43650 -
obs0.191 45975 92.3 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.44 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso max: 97.55 Å2 / Biso mean: 43.02 Å2 / Biso min: 19.33 Å2
Baniso -1Baniso -2Baniso -3
1--12.6395 Å20 Å24.5812 Å2
2--14.4327 Å20 Å2
3----1.7932 Å2
Refinement stepCycle: final / Resolution: 2.39→37.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10152 0 172 286 10610
Biso mean--42.94 39.68 -
Num. residues----1344
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3942-2.44310.35591150.23472226234181
2.4431-2.49620.3621340.23682290242484
2.4962-2.55420.38781330.24492382251586
2.5542-2.61810.32211340.24092382251688
2.6181-2.68880.3791400.24372426256688
2.6888-2.76790.34641190.22712493261289
2.7679-2.85720.33541350.20992475261090
2.8572-2.95930.26751250.20392538266391
2.9593-3.07780.30471390.2022575271493
3.0778-3.21780.29891250.21522655278095
3.2178-3.38730.28741370.19782690282796
3.3873-3.59940.29681450.19272676282197
3.5994-3.8770.23351550.17282717287298
3.877-4.26670.23931430.15152682282597
4.2667-4.88290.20071460.14032773291998
4.8829-6.14740.22811500.17942792294299
6.1474-37.1560.22341500.16812878302899

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