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- PDB-8har: SAH-bound C-Methyltransferase Fur6 from Streptomyces sp. KO-3988 -

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Basic information

Entry
Database: PDB / ID: 8har
TitleSAH-bound C-Methyltransferase Fur6 from Streptomyces sp. KO-3988
ComponentsFur6
KeywordsBIOSYNTHETIC PROTEIN / furaquinocin / biosynthesis
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / methylation
Similarity search - Function
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 / Probable methyltransferase
Similarity search - Component
Biological speciesStreptomyces sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.12 Å
AuthorsNoguchi, T. / Nagata, R. / Tomita, T. / Kuzuyama, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16H06453 Japan
Japan Society for the Promotion of Science (JSPS)19J22569 Japan
CitationJournal: Chem Sci / Year: 2025
Title: Biosynthesis of the tetrahydroxynaphthalene-derived meroterpenoid furaquinocin via reductive deamination and intramolecular hydroalkoxylation of an alkene.
Authors: Noguchi, T. / Zhao, F. / Moriwaki, Y. / Yamamoto, H. / Kudo, K. / Nagata, R. / Tomita, T. / Terada, T. / Shimizu, K. / Nishiyama, M. / Kuzuyama, T.
History
DepositionOct 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1May 14, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / pdbx_entry_details
Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fur6
B: Fur6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7885
Polymers76,8972
Non-polymers8913
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8650 Å2
ΔGint-56 kcal/mol
Surface area26130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.980, 91.840, 125.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fur6


Mass: 38448.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. (bacteria) / Strain: KO-3988 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2L6E4
#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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.81 Å3/Da / Density % sol: 56.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG3350, calcium hydroxide, HEPES-NaOH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.12→50 Å / Num. obs: 94785 / % possible obs: 100 % / Redundancy: 8.1 % / CC1/2: 0.984 / Net I/σ(I): 5.93
Reflection shellResolution: 2.12→2.18 Å / Num. unique obs: 6960 / CC1/2: 0.813 / Rsym value: 0.687

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.12→48.134 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.379 / SU ML: 0.143 / Cross valid method: FREE R-VALUE / ESU R: 0.212 / ESU R Free: 0.188
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2561 2462 4.947 %
Rwork0.2115 47306 -
all0.214 --
obs-49768 99.878 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å2-0 Å20 Å2
2--1.274 Å2-0 Å2
3----1.664 Å2
Refinement stepCycle: LAST / Resolution: 2.12→48.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5303 0 60 120 5483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0135472
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175158
X-RAY DIFFRACTIONr_angle_refined_deg1.31.637452
X-RAY DIFFRACTIONr_angle_other_deg1.1981.57711835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.575712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81723.866238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07715829
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2281518
X-RAY DIFFRACTIONr_chiral_restr0.0570.2732
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026300
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021194
X-RAY DIFFRACTIONr_nbd_refined0.1890.2961
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1640.24438
X-RAY DIFFRACTIONr_nbtor_refined0.1510.22619
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.22406
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2165
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0090.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1370.22
X-RAY DIFFRACTIONr_nbd_other0.2080.214
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1570.24
X-RAY DIFFRACTIONr_mcbond_it1.8664.0612861
X-RAY DIFFRACTIONr_mcbond_other1.8664.0612861
X-RAY DIFFRACTIONr_mcangle_it2.7386.0783568
X-RAY DIFFRACTIONr_mcangle_other2.7386.0793569
X-RAY DIFFRACTIONr_scbond_it2.0744.2072611
X-RAY DIFFRACTIONr_scbond_other2.0734.2072611
X-RAY DIFFRACTIONr_scangle_it3.2916.2393884
X-RAY DIFFRACTIONr_scangle_other3.2916.2393885
X-RAY DIFFRACTIONr_lrange_it4.40247.2115701
X-RAY DIFFRACTIONr_lrange_other4.447.1955689
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.1750.2651670.2513419X-RAY DIFFRACTION99.5282
2.175-2.2350.3091640.2483399X-RAY DIFFRACTION99.776
2.235-2.2990.2781770.2383259X-RAY DIFFRACTION99.7098
2.299-2.370.2711810.2243147X-RAY DIFFRACTION99.7901
2.37-2.4480.2361570.2123084X-RAY DIFFRACTION99.9075
2.448-2.5330.2841610.212992X-RAY DIFFRACTION99.8733
2.533-2.6290.2721660.2172880X-RAY DIFFRACTION99.9016
2.629-2.7360.251560.2132775X-RAY DIFFRACTION99.9659
2.736-2.8580.2921330.2192685X-RAY DIFFRACTION100
2.858-2.9970.2221280.2142564X-RAY DIFFRACTION100
2.997-3.1590.2921380.2242435X-RAY DIFFRACTION100
3.159-3.350.2441210.2172295X-RAY DIFFRACTION100
3.35-3.5810.2271150.2082212X-RAY DIFFRACTION100
3.581-3.8670.2361050.1942023X-RAY DIFFRACTION100
3.867-4.2350.226760.1871915X-RAY DIFFRACTION100
4.235-4.7330.234700.1781740X-RAY DIFFRACTION99.9448
4.733-5.4610.26860.1941524X-RAY DIFFRACTION100
5.461-6.680.261650.231307X-RAY DIFFRACTION100
6.68-9.4080.247670.2211030X-RAY DIFFRACTION100
9.408-48.1340.34290.258621X-RAY DIFFRACTION98.9345

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