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- PDB-9j56: Functional Investigation of the SAM-Dependent Methyltransferases ... -

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Basic information

Entry
Database: PDB / ID: 9j56
TitleFunctional Investigation of the SAM-Dependent Methyltransferases Rdmb in Anthracycline Biosynthesis
ComponentsAclacinomycin 10-hydroxylase RdmB
KeywordsTRANSFERASE / Methyltransferase domain-containing protein / RdmB
Function / homology
Function and homology information


Lyases; Carbon-carbon lyases; Carboxy-lyases / carboxy-lyase activity / O-methyltransferase activity / antibiotic biosynthetic process / Transferases; Transferring one-carbon groups; Methyltransferases / protein dimerization activity
Similarity search - Function
Plant methyltransferase dimerisation / O-methyltransferase dimerisation domain / O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
: / S-ADENOSYL-L-HOMOCYSTEINE / Aclacinomycin 10-hydroxylase RdmB
Similarity search - Component
Biological speciesStreptomyces purpurascens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYang, Q.Y. / Sang, M.L. / Zhang, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Synth Syst Biotechnol / Year: 2025
Title: Functional investigation of the SAM-dependent methyltransferase RdmB in anthracycline biosynthesis.
Authors: Sang, M. / Yang, Q. / Guo, J. / Feng, P. / Ma, W. / Zhang, W.
History
DepositionAug 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aclacinomycin 10-hydroxylase RdmB
B: Aclacinomycin 10-hydroxylase RdmB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4726
Polymers79,6762
Non-polymers1,7964
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-60 kcal/mol
Surface area25800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.997, 79.997, 234.203
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Aclacinomycin 10-hydroxylase RdmB / 15-demethoxy-epsilon-rhodomycin 10-hydroxylase / 15-demethoxyaclacinomycin T


Mass: 39837.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces purpurascens (bacteria) / Gene: rdmB / Production host: Escherichia coli (E. coli)
References: UniProt: Q54527, Lyases; Carbon-carbon lyases; Carboxy-lyases
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1L3V / (7~{S},9~{S})-7-[(2~{R},4~{S},5~{S},6~{S})-4-azanyl-6-methyl-5-oxidanyl-oxan-2-yl]oxy-9-ethyl-4-methoxy-6,9,11-tris(oxidanyl)-8,10-dihydro-7~{H}-tetracene-5,12-dione


Mass: 513.536 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H31NO9 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.72 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: 0.1 M BIS-TRIS pH 6.5, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.1→44.75 Å / Num. obs: 49588 / % possible obs: 95.51 % / Redundancy: 2 % / CC1/2: 1 / Rmerge(I) obs: 0.01634 / Net I/σ(I): 20.1
Reflection shellResolution: 2.1→2.175 Å / Num. unique obs: 5052 / CC1/2: 0.914

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→44.719 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2588 --
Rwork0.214 --
obs-49588 95.54 %
Refinement stepCycle: LAST / Resolution: 2.1→44.719 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4915 0 126 229 5270

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