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- PDB-9vtb: Crystal structure of FjoF bound with GSPP -

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Basic information

Entry
Database: PDB / ID: 9vtb
TitleCrystal structure of FjoF bound with GSPP
ComponentsFjoF
KeywordsTRANSFERASE / prenyltransferase
Function / homologyGERANYL S-THIOLODIPHOSPHATE
Function and homology information
Biological speciesFlavobacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsInoue, S. / Hamada, K. / Goto, Y. / Suga, H. / Sengoku, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) 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: FjoF
B: FjoF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9764
Polymers66,3162
Non-polymers6612
Water10,124562
1
A: FjoF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4882
Polymers33,1581
Non-polymers3301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FjoF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4882
Polymers33,1581
Non-polymers3301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.173, 76.106, 114.216
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein FjoF


Mass: 33157.910 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Uniparc:UPI001229270A / Source: (gene. exp.) Flavobacterium (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GST / GERANYL S-THIOLODIPHOSPHATE / S-[(2E)-3,7-DIMETHYLOCTA-2,6-DIENYL] TRIHYDROGEN THIODIPHOSPHATE


Mass: 330.275 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C10H20O6P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 562 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 100 mM MES pH 6, 200 mM ammonium acetate, 21.4% 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: Jun 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.52→45.02 Å / Num. obs: 99374 / % possible obs: 99.97 % / Redundancy: 68.1 % / Biso Wilson estimate: 15.15 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.6
Reflection shellResolution: 1.52→1.574 Å / Num. unique obs: 9739 / CC1/2: 0.554

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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: 1.52→45.02 Å / SU ML: 0.1803 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.578
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2052 2003 2.02 %
Rwork0.1824 97371 -
obs0.1829 99374 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.48 Å2
Refinement stepCycle: LAST / Resolution: 1.52→45.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4608 0 38 562 5208
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00764781
X-RAY DIFFRACTIONf_angle_d1.02246447
X-RAY DIFFRACTIONf_chiral_restr0.0631697
X-RAY DIFFRACTIONf_plane_restr0.0076822
X-RAY DIFFRACTIONf_dihedral_angle_d5.731634
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.550.33061410.32686776X-RAY DIFFRACTION97.75
1.55-1.60.32571420.26646857X-RAY DIFFRACTION100
1.6-1.640.23381380.23676889X-RAY DIFFRACTION100
1.64-1.70.25231430.21976888X-RAY DIFFRACTION100
1.7-1.760.25371540.22396895X-RAY DIFFRACTION100
1.76-1.830.22091380.19136920X-RAY DIFFRACTION99.99
1.83-1.910.21311410.18326925X-RAY DIFFRACTION100
1.91-2.010.20781360.17376924X-RAY DIFFRACTION99.99
2.01-2.140.19331450.17156956X-RAY DIFFRACTION100
2.14-2.30.19111410.17426958X-RAY DIFFRACTION100
2.3-2.530.20881470.17726980X-RAY DIFFRACTION100
2.53-2.90.21291390.18457009X-RAY DIFFRACTION100
2.9-3.650.19241470.16967094X-RAY DIFFRACTION100
3.65-45.020.1671510.1557300X-RAY DIFFRACTION99.71
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)
11.63373226264-0.127057379439-0.8496127981532.495490216730.2287907030461.921511128760.0506934150743-0.04979063852340.04766796642720.207318621687-0.0650577277730.202028216784-0.0796177506515-0.1587972801740.01100340950750.1205363452660.0154244740129-0.0003026278574510.102337663368-0.007612857252010.1110106052380.167260426446-15.6688746947-8.73689004137
21.80623602287-0.548044212492-0.24024562281.56731925330.2814746713631.03219411016-0.01585148142950.11482609683-0.103281165844-0.0725681569304-0.09025330795230.2294665026810.00667776348301-0.1656377618810.06215903625250.0989488904813-0.00658978043916-0.05144000001410.10430870280.01774947427630.1373763231153.97958792898-31.2036995277-17.8758302034
31.69963973845-1.1054870316-1.001633344092.071140236060.01895835390662.12093252790.1311025150490.09770284438910.291969977251-0.0531376870367-0.0620329483673-0.317727473878-0.183805709130.0682226193897-0.03400376303710.112905995714-0.0180884504477-0.005736247981710.1194792710610.04697111719180.13955376192315.7535052018-17.6480084917-26.2760516846
44.460473496310.123445104002-0.2823533362452.93432177511-0.8052417736182.447526773010.182530183532-0.394149774586-0.1028186575360.39036174519-0.1936566331780.0414585174853-0.2266399414810.1775364641220.00719039445150.154878267954-0.0117562409520.01739997892240.144468610250.02322617094950.096693462636840.048360879-57.97088913333.14461624904
51.29915800981-0.7984282325170.2022421208092.594182594290.1900061101071.06857145345-0.02589925649740.05984196763030.06364429021830.0065921064476-0.0326698127494-0.0243832561682-0.04096109277710.1115603451720.06078022551250.06078585658230.00379589583590.001888827188240.09811126503340.009999612967370.075532287441843.7538703525-44.3583141159-4.92472862718
62.65627517677-0.3570577043190.7742450770220.577204715544-0.3035950663130.30672011947-0.06261861358110.2984622457030.0280952778692-0.070448441844-0.00812353178972-0.00440888401339-0.001037862543180.1038542401950.0425935554580.08908332701880.005664670133050.0016013537310.1141205183470.01320181669240.081987581804636.2955891788-44.2628196825-15.5984490196
71.57525501437-0.574926910581.155406524781.62947598548-0.8520051306852.263320510240.1727602866350.231554058167-0.317352947686-0.366222865611-0.03149243186960.2119445865710.3420426363290.0887688752587-0.0722978231080.168363313460.0175989213787-0.02362001036430.13529506717-0.05080191645850.13450503516527.6073235009-59.3058111566-17.3203846848
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 7 through 87 )AA7 - 873 - 83
22chain 'A' and (resid 88 through 191 )AA88 - 19184 - 187
33chain 'A' and (resid 192 through 283 )AA192 - 283188 - 279
44chain 'B' and (resid 7 through 53 )BC7 - 533 - 49
55chain 'B' and (resid 54 through 118 )BC54 - 11850 - 114
66chain 'B' and (resid 119 through 191 )BC119 - 191115 - 187
77chain 'B' and (resid 192 through 283 )BC192 - 283188 - 279

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