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- PDB-7wdq: DsyB in complex with SAM -

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Basic information

Entry
Database: PDB / ID: 7wdq
TitleDsyB in complex with SAM
ComponentsSAM-dependent MTHB methyltransferase
KeywordsTRANSFERASE / Complex / SAM-dependent methyltransferase
Function / homologyS-ADENOSYLMETHIONINE
Function and homology information
Biological speciesNisaea denitrificans DSM 18348 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 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.pdbx_database_id_DOI / _citation.title
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SAM-dependent MTHB methyltransferase
B: SAM-dependent MTHB methyltransferase
C: SAM-dependent MTHB methyltransferase
D: SAM-dependent MTHB methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,9397
Polymers144,7444
Non-polymers1,1953
Water4,450247
1
A: SAM-dependent MTHB methyltransferase
C: SAM-dependent MTHB methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1694
Polymers72,3722
Non-polymers7972
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-64 kcal/mol
Surface area25120 Å2
MethodPISA
2
B: SAM-dependent MTHB methyltransferase
D: SAM-dependent MTHB methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7703
Polymers72,3722
Non-polymers3981
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-65 kcal/mol
Surface area24890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.490, 115.931, 153.097
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
SAM-dependent MTHB methyltransferase


Mass: 36185.961 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-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H22N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.34 Å3/Da / Density % sol: 47.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M NaCl, 0.1 M Hepes (pH 7.5) and 25% (wt/vol) polyethylene glycol (PEG) 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.987 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: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 56091 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 38.45 Å2 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.035 / Rrim(I) all: 0.093 / Χ2: 3.243 / Net I/σ(I): 15.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.4970.49555360.9190.2010.5352.565100
2.49-2.5970.40555280.9440.1650.4382.69699.9
2.59-2.770.31855580.9630.1280.3432.659100
2.7-2.8570.24355250.9770.0980.2622.812100
2.85-3.0270.17855800.9870.0720.1923.074100
3.02-3.266.80.13255890.9920.0540.1433.468100
3.26-3.586.60.09655840.9940.040.1043.887100
3.58-4.16.40.07356190.9960.0310.0794.20799.9
4.101-5.176.50.05556800.9980.0230.063.87399.9
5.171-506.80.04658920.9980.0190.053.34399.3

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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: SAD / Resolution: 2.35→31.94 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2533 2726 5.08 %
Rwork0.1923 50894 -
obs0.1955 53620 93.38 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.893 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso max: 115.06 Å2 / Biso mean: 46.9 Å2 / Biso min: 19.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.468 Å20 Å2-0 Å2
2--3.6514 Å20 Å2
3----5.1194 Å2
Refinement stepCycle: final / Resolution: 2.35→31.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9982 0 81 247 10310
Biso mean--45.25 39.86 -
Num. residues----1323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810284
X-RAY DIFFRACTIONf_angle_d1.15613970
X-RAY DIFFRACTIONf_chiral_restr0.0781588
X-RAY DIFFRACTIONf_plane_restr0.0041813
X-RAY DIFFRACTIONf_dihedral_angle_d16.4373736
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3502-2.39290.3311630.2513140449
2.3929-2.43890.32341470.2246251190
2.4389-2.48870.29381220.2112256890
2.4887-2.54280.31951320.2284253390
2.5428-2.60190.33661530.2495260092
2.6019-2.66690.35951520.2416262793
2.6669-2.7390.31571230.2306268293
2.739-2.81960.31651550.2317265894
2.8196-2.91050.29541270.2304271095
2.9105-3.01450.35081370.2274271895
3.0145-3.13510.29561480.2207278897
3.1351-3.27760.27271360.2217280398
3.2776-3.45020.26961830.2134280199
3.4502-3.66610.2471440.196287799
3.6661-3.94870.25091520.1877284399
3.9487-4.34520.21161690.16272881100
4.3452-4.97190.19761430.14552905100
4.9719-6.25630.23381710.17932933100
6.2563-31.940.18731690.1573305299

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