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- PDB-9vtd: Crystal structure of MaeF bound with DMASPP -

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Basic information

Entry
Database: PDB / ID: 9vtd
TitleCrystal structure of MaeF bound with DMASPP
ComponentsLynF/TruF/PatF family peptide O-prenyltransferase
KeywordsTRANSFERASE / Peptide Prenyltransferase
Function / homologyPeptide O-prenyltransferase, LynF/TruF/PatF family / Family of unknown function (DUF5838) / transferase activity / DIMETHYLALLYL S-THIOLODIPHOSPHATE / LynF/TruF/PatF family peptide O-prenyltransferase
Function and homology information
Biological speciesMicrocystis aeruginosa BLCC-F108 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsIto, S. / Hamada, K. / Inoue, S. / Suga, H. / Goto, Y. / Sengoku, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Nat Catal
Title: Rapid screening platform for peptide prenyltransferases to diversify pseudo-natural prenylated peptides
Authors: Inoue, S.
History
DepositionJul 10, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 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: LynF/TruF/PatF family peptide O-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3933
Polymers33,0111
Non-polymers3822
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint6 kcal/mol
Surface area13340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.490, 119.490, 78.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-461-

HOH

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Components

#1: Protein LynF/TruF/PatF family peptide O-prenyltransferase


Mass: 33010.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microcystis aeruginosa BLCC-F108 (bacteria)
Strain: BLCCF108 / Gene: H0902_01565 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: A0A841ULY2
#2: Chemical ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O6P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.12 Å3/Da / Density % sol: 41.92 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: Potassium Thiocyanate, PEGMME2000, magnesium chloride Tris-HCl

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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: Apr 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→37.79 Å / Num. obs: 39686 / % possible obs: 99.48 % / Redundancy: 119 % / Biso Wilson estimate: 29.17 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.2121 / Net I/σ(I): 22.89
Reflection shellResolution: 1.57→1.61 Å / Num. unique obs: 2805 / CC1/2: 0.558

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 1.57→37.79 Å / SU ML: 0.2276 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.3823
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.233 2000 5.07 %
Rwork0.1868 37476 -
obs0.1892 39476 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.68 Å2
Refinement stepCycle: LAST / Resolution: 1.57→37.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2308 0 22 104 2434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01782472
X-RAY DIFFRACTIONf_angle_d1.45293351
X-RAY DIFFRACTIONf_chiral_restr0.0909362
X-RAY DIFFRACTIONf_plane_restr0.0131434
X-RAY DIFFRACTIONf_dihedral_angle_d18.3229942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.610.41391310.36172472X-RAY DIFFRACTION92.8
1.61-1.650.27111410.26532614X-RAY DIFFRACTION99.89
1.65-1.70.30021430.26182686X-RAY DIFFRACTION100
1.7-1.760.36521410.26882644X-RAY DIFFRACTION100
1.76-1.820.29251420.24022665X-RAY DIFFRACTION100
1.82-1.890.27671420.1932649X-RAY DIFFRACTION100
1.89-1.980.23831430.18152680X-RAY DIFFRACTION100
1.98-2.080.21491410.17542662X-RAY DIFFRACTION100
2.08-2.210.23991440.18412691X-RAY DIFFRACTION100
2.21-2.380.21241440.17092695X-RAY DIFFRACTION100
2.38-2.620.24881430.17542689X-RAY DIFFRACTION100
2.62-30.2241450.18072720X-RAY DIFFRACTION100
3-3.780.23311460.18012742X-RAY DIFFRACTION100
3.78-37.790.21221540.1822867X-RAY DIFFRACTION99.93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.213451568221.33239208096-0.5137491229052.604291632220.7315501487323.51120266778-0.08305385021470.207601084187-0.1445105818370.05972061304620.146703174327-0.1098119955970.08302503212350.246574950542-0.02556457827150.130040125367-0.003008557204110.00920793669750.185344250982-0.02979448120340.17835085197238.2235353675-4.9790674091213.4727714545
23.58746095204-0.632211798855-0.4041402912122.43395262646-1.447780032253.262983381970.05441670380920.02799944767650.5111948443040.1405275624810.2656241767350.0220674969475-0.619861701813-0.292445447101-0.1680531990870.3334383705880.03578193090380.05662170505550.2321559297440.01886297979970.28393379190731.36294154399.1426049026410.2025587711
32.602193816370.0616616755095-2.557058743650.861504902326-0.7967877713052.208782188310.2079905490990.4004830082730.3881772054930.1031422887640.02228748294850.133813454014-0.523745409759-0.353218402586-0.2120140524610.351527400650.05158436191970.002133123527120.3903358445890.06140791277360.31894583709819.89546678868.3045212642312.663270774
42.77607706151-0.41422212768-1.318658763833.912711371511.587911766672.9461818514-0.02930069782310.4655711172220.0700460590385-0.3223381098720.005731124466370.691794584721-0.160342483316-0.749670349343-0.02093540195920.2440674805780.00154546700293-0.03149141868310.3950378148750.03995972741240.31216096055812.2270227747-2.629634380617.126500642
52.984850755390.912757797763-0.4230664537353.418997720730.669686808673.09187421943-0.2529144726010.354950701036-0.468702380593-0.03144642681670.05953911128890.1865524714930.408893785007-0.714309474241-0.1423737031880.223716251471-0.1225649221640.03950285836130.314372451727-0.06794971123270.24570716720619.7267423367-13.444993370913.282766021
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 8 through 88 )8 - 881 - 81
22chain 'A' and (resid 89 through 149 )89 - 14982 - 142
33chain 'A' and (resid 150 through 191 )150 - 191143 - 184
44chain 'A' and (resid 192 through 248 )192 - 248185 - 241
55chain 'A' and (resid 249 through 289 )249 - 289242 - 282

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