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- PDB-9vte: Crystal structure of AphF bound with DMASPP -

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Basic information

Entry
Database: PDB / ID: 9vte
TitleCrystal structure of AphF bound with DMASPP
ComponentsLynF/TruF/PatF family peptide O-prenyltransferase
KeywordsTRANSFERASE / Peptide Prenyltransferase
Function / homologyDIMETHYLALLYL S-THIOLODIPHOSPHATE / DI(HYDROXYETHYL)ETHER / :
Function and homology information
Biological speciesAphanizomenon sp. UHCC 0183 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 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
B: LynF/TruF/PatF family peptide O-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2328
Polymers66,5282
Non-polymers7036
Water1,51384
1
A: LynF/TruF/PatF family peptide O-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5513
Polymers33,2641
Non-polymers2862
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LynF/TruF/PatF family peptide O-prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6815
Polymers33,2641
Non-polymers4174
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.130, 94.530, 87.780
Angle α, β, γ (deg.)90.000, 92.520, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 8 or (resid 9 and (name...
d_2ens_1(chain "B" and (resid 8 through 23 or resid 25...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLYGLYILEILEAA8 - 2893 - 284
d_12DSTDSTDSTDSTAC301
d_21GLYGLYILEILEBB8 - 233 - 18
d_22ASNASNGLYGLYBB25 - 10420 - 99
d_23ASPASPILEILEBB106 - 289101 - 284
d_24DSTDSTDSTDSTBE301

NCS oper: (Code: givenMatrix: (-0.995716640101, -0.00490397595244, -0.0923272638269), (0.00505731025359, -0.999986193721, -0.00142687784093), (-0.0923189917564, -0.00188769362764, 0.995727693887) ...NCS oper: (Code: given
Matrix: (-0.995716640101, -0.00490397595244, -0.0923272638269), (0.00505731025359, -0.999986193721, -0.00142687784093), (-0.0923189917564, -0.00188769362764, 0.995727693887)
Vector: -1.78013031165, -4.38707285808, 43.8285989526)

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Components

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


Mass: 33264.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aphanizomenon sp. UHCC 0183 (bacteria) / Gene: FJR37_04620 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: A0A844I5Y0
#2: Chemical ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O6P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.25 Å3/Da / Density % sol: 45.36 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: magnesium chloride, Bis-Tris, PEG3350

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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: Jan 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.76→43.85 Å / Num. obs: 15228 / % possible obs: 99.88 % / Redundancy: 64 % / Biso Wilson estimate: 20.08 Å2 / CC1/2: 0.937 / Net I/σ(I): 5.59
Reflection shellResolution: 2.76→2.859 Å / Num. unique obs: 1495 / CC1/2: 0.523

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.76→43.85 Å / SU ML: 0.3755 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.1041
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2985 1520 9.99 %
Rwork0.2414 13694 -
obs0.247 15214 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.8 Å2
Refinement stepCycle: LAST / Resolution: 2.76→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4621 0 38 84 4743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00384747
X-RAY DIFFRACTIONf_angle_d0.6886409
X-RAY DIFFRACTIONf_chiral_restr0.0463708
X-RAY DIFFRACTIONf_plane_restr0.0053819
X-RAY DIFFRACTIONf_dihedral_angle_d4.8827631
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.898461772133 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-2.850.34451310.29311225X-RAY DIFFRACTION99.93
2.85-2.950.33121570.27881222X-RAY DIFFRACTION100
2.95-3.070.34481370.2911253X-RAY DIFFRACTION99.86
3.07-3.210.32661330.27271226X-RAY DIFFRACTION100
3.21-3.380.32081410.26021251X-RAY DIFFRACTION100
3.38-3.590.37481350.24641267X-RAY DIFFRACTION100
3.59-3.870.29681380.23291213X-RAY DIFFRACTION100
3.87-4.260.29861420.22151245X-RAY DIFFRACTION99.86
4.26-4.870.24051330.19631247X-RAY DIFFRACTION99.93
4.87-6.130.23781350.22041274X-RAY DIFFRACTION100
6.13-43.850.24251380.21671271X-RAY DIFFRACTION99.44
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)
10.392811707683-0.358361955279-0.006431287655310.539344687774-0.1660090438240.136058960788-0.0981556912203-0.122808507017-0.1664364734810.1619389843340.08850850904240.04615887075930.0299466438623-0.29681343210.009400977173540.366600997842-0.115686764881-0.0243614815710.36293470243-0.0540310357640.1705096837470.461980034653-9.272390364281.33871319211
20.460179834338-0.2181965446270.4342015333190.171238218863-0.05883318387760.815276641313-0.0398448594694-0.124831672298-0.509175159342-0.140161849078-0.0162740798885-0.118703946876-0.0295728891568-0.2332269543210.01081335334790.355112864052-0.02960038682580.05892424555910.152192857345-0.04993389581070.204466705861-2.13221489355-8.6502390134410.8889889672
30.015640690812-0.06221972630630.05997882835070.242384467409-0.2315951237980.2225791433670.107976081841-0.04796828241860.1421769300650.1282364305620.1075185281050.24657957079-0.100019384595-0.1108830331130.2451080195750.1233920991290.01758721530740.09802541691660.05429727096460.04801984782840.585680666691-5.86987316494-21.210823974718.139281701
40.1280816630240.07612398780060.1143248826060.225447090751-0.118032897130.2898861658380.04545937190630.0157112226657-0.01771934393040.03731828580890.06865646811710.1360343339460.0310215280525-0.2482853246480.3589855980610.137201088085-0.1179079648180.1097687899880.1945993203030.01588942796670.32422508178-2.17371925087-18.035281969125.9877095596
50.2122585876920.040090514527-0.2319692657380.3391988491590.105756453640.3152235971890.0413723108461-0.0583550455681-0.1066549172890.00626573120925-0.00975892271214-0.1113401031785.08620533674E-50.03736047111480.09770479843860.0725443123481-0.006088365097290.1024301178720.223261988484-0.02212386881730.2099060484772.99746873355-11.489928076415.614863558
60.9528245641450.236522274701-0.432494782091.064198600570.4570421067881.043722156340.188733471955-0.2721443750590.00348960661820.0156520995334-0.0113871939211-0.207738625963-0.3744506591670.2347640486850.4729878703140.304287342067-0.0391334162340.01837699182140.07403184834240.06845737988330.03588944645790.990563335348-5.6750248470430.7715642795
70.738823696652-0.2685179349360.2867990341540.132666144124-0.1409590397330.155552612435-0.0801376127867-0.220074667480.242770075158-0.01694824571290.180708502017-0.0773950370831-0.211854350241-0.09884783535780.1162113439490.483010359269-0.1164480501450.08114308454790.183528199269-0.1311367852660.06068188578984.016502145389.6854591956727.3774111226
80.1998382569050.0078096771425-0.1193649097640.0515757278899-0.003599244021470.175048357240.05842910579610.0122906364089-0.128697204392-0.1502837466740.137996437206-0.0830659796374-0.1825624046860.1618137130850.03204416873860.401609732790.00655913876642-0.01422844876060.0781182971503-0.03705733622060.1956984229247.578600294077.2720802154411.7999799797
90.8988792498470.289479635515-0.4864623493940.608410523717-0.6148665639780.8729408947320.2033892928360.2690326195410.107694494104-0.2650181208940.0677851612132-0.0923639613703-0.18798555891-0.06926019217440.5955129305820.329943389998-0.07805885315910.1452155336380.205801235762-0.1253106534990.01325141458577.753850042125.1992680676413.3527574221
100.216513733552-0.0248533644353-0.2317396104690.135303610393-0.1511835497330.4905316944820.0519631527474-0.1103115314840.09876612231530.08457946086430.011339316210.012718424129-0.1356951180390.2459045406520.3643844601350.458889893595-0.04047068128180.04845199161880.2950826613430.0329709234680.0737402581436-2.867799424295.2171609365444.9396614508
110.473253143966-0.06339410635630.279499330920.353843772994-0.1875318430630.229495071673-0.1141808110740.1137769147640.485246168764-0.0522405967907-0.254988450997-0.227079126405-0.07354754280680.237922257773-0.2844026179150.1210571715320.02147980539240.00341629499650.2630343756650.1407873637560.3223511951332.237541675015.3817310944354.4866293362
120.133690023225-0.167366542489-0.06691327702930.394493577745-0.01355104025350.09002877374040.0395416552695-0.06198874152980.2357926712330.1054877553730.0850709118766-0.10449366390.009546129851360.02914718241920.6638718295110.180743784185-0.0739733472837-0.135190652521-0.0646457071956-0.0074436930920.461268204906-1.194001828869.5288291453559.2624780574
130.229302382912-0.127345837629-0.2268263018120.2956619382480.01784320546930.4708791052170.0389582208965-0.07529477137640.1569513320230.08191399505350.0797538222306-0.004241726063160.03166432928050.07968213020740.1779535043930.113778614677-0.0966414673186-0.1153378153490.1067996332180.0251904742310.186201482042-1.6773754896113.708214872570.4389000237
140.3086763668410.1275017812340.02654189024250.431061759761-0.02594563883860.851462916750.155331392959-0.0651544680283-0.065294188034-0.0215919372444-0.2783347639830.1558742884160.37505108369-0.115925494972-0.06962753799450.152247183415-0.01813358125770.007239091864940.223814749037-0.04013679444560.165844643669-5.92570216827-2.1639684222971.4556678731
150.09619408704990.0447937752126-0.001717302632440.2059387416950.01882846802040.05497767454180.04199119770510.0951527193461-0.0487380767379-0.00162710374118-0.04923353984180.1307643570470.0115294548744-0.07564071213110.04856414391990.0617039666215-0.07532269451370.01926054810170.177667458848-0.03270375584210.203086763505-11.0422476325-13.48333928261.6721039251
160.0592204336652-0.1826728943360.01175583150940.553004801544-0.06156650446750.03422143930480.142538626704-0.0758453570782-0.187656199945-0.277976948881-0.1719585141350.1023758308090.110318056148-0.1182600585180.02564948166790.218874555798-0.118762758613-0.03232654369150.1471293065510.01946589438040.128798111423-10.1169279355-9.7153092439153.2962163641
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 8 through 28 )AA8 - 281 - 20
22chain 'A' and (resid 29 through 72 )AA29 - 7221 - 64
33chain 'A' and (resid 73 through 88 )AA73 - 8865 - 80
44chain 'A' and (resid 89 through 111 )AA89 - 11181 - 102
55chain 'A' and (resid 112 through 128 )AA112 - 128103 - 119
66chain 'A' and (resid 129 through 177 )AA129 - 177120 - 168
77chain 'A' and (resid 178 through 222 )AA178 - 222169 - 213
88chain 'A' and (resid 223 through 260 )AA223 - 260214 - 251
99chain 'A' and (resid 261 through 289 )AA261 - 289252 - 280
1010chain 'B' and (resid 8 through 28 )BD8 - 281 - 21
1111chain 'B' and (resid 29 through 55 )BD29 - 5522 - 48
1212chain 'B' and (resid 56 through 88 )BD56 - 8849 - 81
1313chain 'B' and (resid 89 through 111 )BD89 - 11182 - 104
1414chain 'B' and (resid 112 through 203 )BD112 - 203105 - 196
1515chain 'B' and (resid 204 through 250 )BD204 - 250197 - 243
1616chain 'B' and (resid 251 through 289 )BD251 - 289244 - 282

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