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Basic information

Entry
Database: PDB / ID: 9la8
TitleComparative analysis of functions and catalytic mechanisms of methyltransferases involved in anthracycline biosynthesis
ComponentsMethyltransferase domain-containing protein
KeywordsTRANSFERASE / DnrK
Function / homology
Function and homology information


O-methyltransferase activity / antibiotic biosynthetic process / methylation / 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 / Methyltransferase domain-containing protein
Similarity search - Component
Biological speciesStreptomyces coeruleorubidus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsYang, Q.Y. / Sang, M.L. / Zhang, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Comparative analysis of functions and catalytic mechanisms of methyltransferases involved in anthracycline biosynthesis
Authors: Yang, Q.Y. / Sang, M.L. / Zhang, W.
History
DepositionJan 1, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 7, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methyltransferase domain-containing protein
B: Methyltransferase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,8596
Polymers82,0632
Non-polymers1,7964
Water18,3031016
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-49 kcal/mol
Surface area24650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.401, 101.708, 62.433
Angle α, β, γ (deg.)90.000, 102.547, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Methyltransferase domain-containing protein


Mass: 41031.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coeruleorubidus (bacteria)
Gene: CP976_32885 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5J6IBS5
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: isolated from a natural source / 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.: 1016 / 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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M BIS-TRIS (pH 5.5), 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: 1.29→58.96 Å / Num. obs: 104403 / % possible obs: 99.96 % / Redundancy: 5.8 % / CC1/2: 0.993 / Net I/σ(I): 11.1
Reflection shellResolution: 1.29→1.36 Å / Num. unique obs: 10376 / CC1/2: 0.873

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
PHENIX1.19.1_4122refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→38.51 Å / SU ML: 0.1273 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 17.4775
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1839 1405 1.35 %
Rwork0.1601 102998 -
obs0.1604 104403 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.16 Å2
Refinement stepCycle: LAST / Resolution: 1.56→38.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5193 0 126 1016 6335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00695439
X-RAY DIFFRACTIONf_angle_d1.12667440
X-RAY DIFFRACTIONf_chiral_restr0.0602866
X-RAY DIFFRACTIONf_plane_restr0.0106957
X-RAY DIFFRACTIONf_dihedral_angle_d5.7852750
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.620.18071460.155710230X-RAY DIFFRACTION100
1.62-1.680.2081340.162910323X-RAY DIFFRACTION99.99
1.68-1.760.20251330.16310243X-RAY DIFFRACTION99.98
1.76-1.850.20891460.173410278X-RAY DIFFRACTION100
1.85-1.970.18571360.162810279X-RAY DIFFRACTION99.99
1.97-2.120.18051460.158910277X-RAY DIFFRACTION99.97
2.12-2.330.19881350.156410323X-RAY DIFFRACTION99.96
2.33-2.670.18051420.165610299X-RAY DIFFRACTION99.96
2.67-3.360.19871440.16510334X-RAY DIFFRACTION99.97
3.36-38.510.15831430.152110412X-RAY DIFFRACTION99.83
Refinement TLS params.Method: refined / Origin x: 8.29196848632 Å / Origin y: 0.442026330258 Å / Origin z: 15.9849109927 Å
111213212223313233
T0.0999939152713 Å20.0112914191461 Å20.000328416729074 Å2-0.115138463795 Å2-8.47842629118E-5 Å2--0.0735093277784 Å2
L0.26868990321 °20.140497985527 °20.0116370866789 °2-0.537852096161 °20.00918985193592 °2--0.15264018947 °2
S0.00286988752929 Å °-0.00853200446276 Å °0.00691918044519 Å °-0.00861249587331 Å °-0.00779933438638 Å °-0.00204174713038 Å °-0.0113538930603 Å °0.0249975712831 Å °1.17813891146E-5 Å °
Refinement TLS groupSelection details: all

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