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- PDB-9vta: Crystal structure of Fl3F bound with GSPP -

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Basic information

Entry
Database: PDB / ID: 9vta
TitleCrystal structure of Fl3F bound with GSPP
ComponentsFl3F
KeywordsTRANSFERASE / prenyltransferase
Function / homologyGERANYL S-THIOLODIPHOSPHATE / :
Function and homology information
Biological speciesFlavobacterium sp. 38-13 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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

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Assembly

Deposited unit
A: Fl3F
B: Fl3F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9464
Polymers66,2862
Non-polymers6612
Water7,927440
1
A: Fl3F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4732
Polymers33,1431
Non-polymers3301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fl3F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4732
Polymers33,1431
Non-polymers3301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.549, 76.290, 114.375
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 Fl3F


Mass: 33142.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium sp. 38-13 (bacteria) / Gene: BGO88_13875 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6N4AFE2
#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: obtained synthetically / Formula: C10H20O6P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 100 mM NaK tartrate tetrahydrate, 22.5% PEG smear broad, 10% v/v ethylene glycol, and 100 mM MES, pH 5.5

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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 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→38.7 Å / Num. obs: 88158 / % possible obs: 99.68 % / Redundancy: 12.6 % / Biso Wilson estimate: 22.64 Å2 / CC1/2: 0.993 / Net I/σ(I): 13.13
Reflection shellResolution: 1.57→1.631 Å / Num. unique obs: 8504 / CC1/2: 0.562

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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: 1.57→38.7 Å / SU ML: 0.2253 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.3004
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2183 1995 2.26 %
Rwork0.1867 86114 -
obs0.1874 88109 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.89 Å2
Refinement stepCycle: LAST / Resolution: 1.57→38.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4599 0 38 440 5077
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00764776
X-RAY DIFFRACTIONf_angle_d0.94666442
X-RAY DIFFRACTIONf_chiral_restr0.0639695
X-RAY DIFFRACTIONf_plane_restr0.0065825
X-RAY DIFFRACTIONf_dihedral_angle_d5.6521633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.610.31771420.30065874X-RAY DIFFRACTION96.61
1.61-1.660.30091360.27046104X-RAY DIFFRACTION99.92
1.66-1.710.28041540.25526072X-RAY DIFFRACTION99.97
1.71-1.760.43251380.31716127X-RAY DIFFRACTION99.97
1.76-1.820.28541380.27176088X-RAY DIFFRACTION99.92
1.82-1.90.30771440.21596111X-RAY DIFFRACTION99.98
1.9-1.980.21611370.17776147X-RAY DIFFRACTION100
1.98-2.090.22831400.17956134X-RAY DIFFRACTION100
2.09-2.220.2091450.18986163X-RAY DIFFRACTION100
2.22-2.390.19751430.16786166X-RAY DIFFRACTION100
2.39-2.630.20591380.18016187X-RAY DIFFRACTION99.98
2.63-3.010.20151490.18216193X-RAY DIFFRACTION99.87
3.01-3.790.21771460.17016256X-RAY DIFFRACTION99.63
3.8-38.70.18041450.16576492X-RAY DIFFRACTION99.73
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)
14.70040184546-0.1296982394450.2183948986354.88366545625-0.4438645963062.699029856210.0635252887748-0.365100767329-0.1427676118260.563425642014-0.126586404702-0.0806144976448-0.1644223735090.04067588595070.0589621885220.1922307632240.008125532607510.003553178235920.1577569847910.0448246053830.12954794679540.1514198682-20.15442663182.67020075243
22.05200072452-0.7167439830080.2604623083323.13312551735-0.1084132971611.45319155446-0.02676093638210.04675426945260.03741986222130.0231398701114-0.0566986695789-0.111483198778-0.02013902369550.1284677600380.09173491948860.134760295605-0.000137161480007-0.001486698019160.1576532488570.01275771886840.13486127062743.4161773847-6.1410865367-4.94557303851
34.93910974097-2.850088049491.205412609176.64207178691-1.804425417922.85986398362-0.1144583113220.0324211284496-0.157339112106-0.04928312959510.00633999429793-0.3595838357310.1120126466150.1519259464580.06409481765260.117628465389-0.01577532020730.01169447964560.101685563018-0.009591392124130.12194237971741.5680917643-9.83301059304-9.46807731788
43.54989029916-0.7109792544721.258873435610.656822393509-0.3217001448340.538384601764-0.05510739456560.3634966731690.0577800704906-0.0864464406258-0.0566069118882-0.0510699181989-0.01030674728490.1575309013420.1055426280450.164001459902-0.00245792169524-0.0005958514698440.1783219320050.02670556180180.14424057833733.8612557653-4.76425062935-17.7825727809
51.58511540945-0.7358683622241.055246770221.94282028606-1.184953458432.299277135550.1192331117680.169066534037-0.330644626875-0.2888854855650.01488692598860.1927869792190.2866306602470.0786620456601-0.1102988058950.205198459073-0.00625663496294-0.005239166480940.156678583571-0.04597989540640.17932309543527.4644798116-21.2855358285-17.3440062202
62.41370864619-0.1761383908260.5136635321911.978289208380.9912314773312.523773216280.1364120380440.0807547264881-0.12998816474-0.131167356599-0.0602076112390.03991989980010.031153347392-0.121033526545-0.07877874591850.177308837415-0.0230655186524-0.01233525316690.1209400416370.0002777202824020.14607181887338.34867760412.77307364319.02505966755
72.187909246180.5410356878440.4082749112411.745311906230.1070956556811.022037981970.0163733449068-0.1862456259560.003483793803390.0468317783104-0.07147211607310.198649990690.00595501099267-0.1398783325640.05464733904090.1593273422020.001691398546210.05160403919820.1564986661430.02123921693970.16196855323442.373701415429.60378826718.1574021165
81.834776200360.7143921139111.348440233942.011986104950.4863432198153.943533147470.227104240826-0.131618644466-0.3709896432920.173460570213-0.00599114794515-0.2637303135390.315431761197-0.00518486498838-0.1546801972490.188367340295-0.00943316869518-0.01715599909790.1376248725770.05801444769510.20608878263849.311890571213.889802195225.9208587088
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 53 )AA8 - 533 - 48
22chain 'A' and (resid 54 through 118 )AA54 - 11849 - 113
33chain 'A' and (resid 119 through 138 )AA119 - 138114 - 133
44chain 'A' and (resid 139 through 191 )AA139 - 191134 - 186
55chain 'A' and (resid 192 through 283 )AA192 - 283187 - 278
66chain 'B' and (resid 5 through 70 )BC5 - 701 - 66
77chain 'B' and (resid 71 through 221 )BC71 - 22167 - 217
88chain 'B' and (resid 222 through 283 )BC222 - 283218 - 279

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