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

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Basic information

Entry
Database: PDB / ID: 8rdo
TitleHolomycin methyltransferase DtpM with SAH and XRD-271Me
ComponentsDtpM
KeywordsTRANSFERASE / N-Methyltransferase / dithiopyrrolone / natural product / xenorabdin
Function / homologyD-MALATE / S-ADENOSYL-L-HOMOCYSTEINE / :
Function and homology information
Biological speciesXenorhabdus doucetiae FRM16 = DSM 17909 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4627
Polymers38,3821
Non-polymers1,0796
Water1,22568
1
A: DtpM
hetero molecules

A: DtpM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,92314
Polymers76,7652
Non-polymers2,15812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/41
Buried area9170 Å2
ΔGint-28 kcal/mol
Surface area25520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.430, 53.430, 209.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-510-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DtpM


Mass: 38382.414 Da / Num. of mol.: 1
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 , 5 types, 74 molecules

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


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


Mass: 284.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H16N2O2S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 1.95 Å3/Da / Density % sol: 36.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.1 M D/L malic acid, pH 7.0

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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: 1.75→47 Å / Num. obs: 31122 / % possible obs: 97.6 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 16.7
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4643 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.955 / SU B: 6.665 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.142 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21981 1555 5 %RANDOM
Rwork0.20324 ---
obs0.20408 29553 97.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.119 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å2-0 Å2-0 Å2
2--0.86 Å2-0 Å2
3----1.73 Å2
Refinement stepCycle: 1 / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2608 0 71 68 2747
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0132773
X-RAY DIFFRACTIONr_bond_other_d0.0010.0142618
X-RAY DIFFRACTIONr_angle_refined_deg1.3131.6573777
X-RAY DIFFRACTIONr_angle_other_deg1.211.5896015
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2755349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.23219.355155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83815425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8721533
X-RAY DIFFRACTIONr_chiral_restr0.0560.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023147
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02632
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_it0.6662.2451387
X-RAY DIFFRACTIONr_mcbond_other0.6662.2451387
X-RAY DIFFRACTIONr_mcangle_it1.1793.3621739
X-RAY DIFFRACTIONr_mcangle_other1.1793.3611740
X-RAY DIFFRACTIONr_scbond_it0.7012.4071385
X-RAY DIFFRACTIONr_scbond_other0.7012.4061384
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1993.5612039
X-RAY DIFFRACTIONr_long_range_B_refined2.65526.7152956
X-RAY DIFFRACTIONr_long_range_B_other2.63926.7022951
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 112 -
Rwork0.307 2125 -
obs--97.18 %
Refinement TLS params.Method: refined / Origin x: 10.394 Å / Origin y: 62.0924 Å / Origin z: 38.7129 Å
111213212223313233
T0.0738 Å2-0.0124 Å20.0041 Å2-0.0173 Å20.0018 Å2--0.0579 Å2
L0.2205 °20.2855 °20.3133 °2-0.4761 °20.6636 °2--1.1375 °2
S-0.0132 Å °0.0225 Å °-0.0467 Å °-0.1023 Å °0.0427 Å °-0.031 Å °-0.2275 Å °0.0274 Å °-0.0296 Å °

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