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- PDB-8rdm: Holomycin methyltransferase DtpM with SAH -

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Basic information

Entry
Database: PDB / ID: 8rdm
TitleHolomycin methyltransferase DtpM with SAH
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: 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)38,9514
Polymers38,3821
Non-polymers5693
Water1,63991
1
A: DtpM
hetero molecules

A: DtpM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9028
Polymers76,7652
Non-polymers1,1376
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/41
Buried area8170 Å2
ΔGint-35 kcal/mol
Surface area26290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.210, 53.210, 207.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#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
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
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: 1.92 Å3/Da / Density % sol: 35.85 %
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: 30822 / % possible obs: 98.4 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.5
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.675 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4611 / % possible all: 98.5

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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: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 7.56 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21912 1540 5 %RANDOM
Rwork0.17593 ---
obs0.17805 29272 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.837 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å2-0 Å2-0 Å2
2--0.44 Å2-0 Å2
3----0.89 Å2
Refinement stepCycle: 1 / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2608 0 38 91 2737
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0132768
X-RAY DIFFRACTIONr_bond_other_d0.0010.0142628
X-RAY DIFFRACTIONr_angle_refined_deg1.2061.6483773
X-RAY DIFFRACTIONr_angle_other_deg1.1431.5776033
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9345353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.59118.938160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75915433
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0891536
X-RAY DIFFRACTIONr_chiral_restr0.0490.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023162
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02649
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_it1.3313.0651397
X-RAY DIFFRACTIONr_mcbond_other1.3313.0651397
X-RAY DIFFRACTIONr_mcangle_it1.8434.5951755
X-RAY DIFFRACTIONr_mcangle_other1.8424.5941756
X-RAY DIFFRACTIONr_scbond_it1.3093.381370
X-RAY DIFFRACTIONr_scbond_other1.3093.381371
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7454.9722019
X-RAY DIFFRACTIONr_long_range_B_refined2.86836.7832949
X-RAY DIFFRACTIONr_long_range_B_other2.66336.7422943
X-RAY DIFFRACTIONr_rigid_bond_restr0.44835394
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
Rfree0.305 110 -
Rwork0.29 2097 -
obs--98 %
Refinement TLS params.Method: refined / Origin x: 10.2339 Å / Origin y: 61.8991 Å / Origin z: 38.4648 Å
111213212223313233
T0.0224 Å2-0.0008 Å2-0.0001 Å2-0.017 Å2-0.0002 Å2--0.0003 Å2
L0.0268 °20.0385 °20.0428 °2-0.0617 °20.0853 °2--0.1639 °2
S-0.004 Å °0.0015 Å °-0.0016 Å °-0.0102 Å °0.0072 Å °-0.0024 Å °-0.0288 Å °0.0121 Å °-0.0032 Å °

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