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- PDB-8rdn: Holomycin methyltransferase DtpM with SAH and XRD-271 -

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Basic information

Entry
Database: PDB / ID: 8rdn
TitleHolomycin methyltransferase DtpM with SAH and XRD-271
ComponentsDtpM
KeywordsTRANSFERASE / N-Methyltransferase / dithiopyrrolone / natural product / xenorabdin
Function / homologyS-ADENOSYL-L-HOMOCYSTEINE / :
Function and homology information
Biological speciesXenorhabdus doucetiae FRM16 = DSM 17909 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHuber, E.M. / Groll, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB1309-325871075 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Isofunctional but Structurally Different Methyltransferases for Dithiolopyrrolone Diversification.
Authors: Su, L. / Huber, E.M. / Westphalen, M. / Gellner, J. / Bode, E. / Kobel, T. / Grun, P. / Alanjary, M.M. / Glatter, T. / Cirnski, K. / Muller, R. / Schindler, D. / Groll, M. / Bode, H.B.
History
DepositionDec 8, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)156,41619
Polymers153,5304
Non-polymers2,88715
Water3,981221
1
A: DtpM
C: DtpM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1338
Polymers76,7652
Non-polymers1,3686
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7700 Å2
ΔGint-48 kcal/mol
Surface area26520 Å2
MethodPISA
2
D: DtpM
hetero molecules

B: DtpM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,28311
Polymers76,7652
Non-polymers1,5199
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
Buried area7980 Å2
ΔGint-64 kcal/mol
Surface area26310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.400, 218.830, 55.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
DtpM


Mass: 38382.414 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenorhabdus doucetiae FRM16 = DSM 17909 (bacteria)
Gene: J7S33_29485 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold

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Non-polymers , 6 types, 236 molecules

#2: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-YRH / ~{N}-(5-oxidanylidene-4~{H}-[1,2]dithiolo[4,3-b]pyrrol-6-yl)hexanamide


Mass: 270.371 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H14N2O2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.22 Å3/Da / Density % sol: 44.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 1 M LiCl2, 0.1 M MES, pH 6.0, 30% PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→49 Å / Num. obs: 64433 / % possible obs: 91.5 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 10.7
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.676 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 8179 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / SU B: 14.659 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.35 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22163 3220 5 %RANDOM
Rwork0.19295 ---
obs0.19438 61187 91.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.506 Å2
Baniso -1Baniso -2Baniso -3
1-3.41 Å20 Å2-0 Å2
2---2.38 Å20 Å2
3----1.03 Å2
Refinement stepCycle: 1 / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10479 0 184 221 10884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01310909
X-RAY DIFFRACTIONr_bond_other_d0.0010.01410310
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.65614844
X-RAY DIFFRACTIONr_angle_other_deg1.1811.58823666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.23551367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.06419.278623
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78151693
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.26315134
X-RAY DIFFRACTIONr_chiral_restr0.0580.21400
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022513
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3023.6745482
X-RAY DIFFRACTIONr_mcbond_other1.3013.6745482
X-RAY DIFFRACTIONr_mcangle_it2.2145.5066845
X-RAY DIFFRACTIONr_mcangle_other2.2145.5066846
X-RAY DIFFRACTIONr_scbond_it1.3673.8955426
X-RAY DIFFRACTIONr_scbond_other1.3673.8955427
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.395.7668000
X-RAY DIFFRACTIONr_long_range_B_refined3.85342.27111315
X-RAY DIFFRACTIONr_long_range_B_other3.8542.24711293
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 241 -
Rwork0.307 4579 -
obs--94.45 %
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)
10.2838-0.25590.2050.4454-0.20390.20440.01950.00040.0432-0.0064-0.0587-0.03470.0320.00820.03920.0834-0.0015-0.00010.01940.00750.027635.807968.251237.0124
20.2470.1644-0.20080.3711-0.10990.27490.01540.00340.0077-0.0277-0.04340.0053-0.01340.01780.0280.10320.0071-0.00390.01650.00840.011137.129339.234616.3748
30.4008-0.1220.2280.4712-0.1170.13920.0415-0.00230.0515-0.0311-0.0645-0.02670.0285-0.00230.0230.0840.0130.01080.02760.01520.017716.48393.978619.5492
40.4954-0.36220.17530.3713-0.08470.1710.08620.058-0.0028-0.0243-0.08560.0024-0.0222-0.0039-0.00060.11980.00760.01090.02590.00190.003874.629195.354920.5629
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 402
2X-RAY DIFFRACTION2B10 - 402
3X-RAY DIFFRACTION3C9 - 402
4X-RAY DIFFRACTION4D5 - 402

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