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- PDB-9v4j: Prenyltransferase Ord1 Wild type-FSPP -

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Basic information

Entry
Database: PDB / ID: 9v4j
TitlePrenyltransferase Ord1 Wild type-FSPP
Componentsprenyltransferase
KeywordsTRANSFERASE / Prenyltransferase
Function / homologyChem-FPS
Function and homology information
Biological speciesStreptomyces sp. KS84 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOshiro, T. / Uehara, S. / Ito, T. / Tanaka, Y. / Kodera, Y. / Matsui, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17KK0141 Japan
Japan Society for the Promotion of Science (JSPS)21K06036 Japan
CitationJournal: Biochemistry / Year: 2025
Title: Structure-Activity Relationship of an All-alpha-helical Prenyltransferase Reveals the Mechanism of Indole Prenylation.
Authors: Oshiro, T. / Uehara, S. / Suto, A. / Tanaka, Y. / Ito, T. / Kodera, Y. / Matsui, T.
History
DepositionMay 23, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: prenyltransferase
B: prenyltransferase
C: prenyltransferase
D: prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,76514
Polymers144,7814
Non-polymers98310
Water3,783210
1
A: prenyltransferase
C: prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6115
Polymers72,3912
Non-polymers2203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: prenyltransferase
D: prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1549
Polymers72,3912
Non-polymers7637
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.100, 72.560, 84.220
Angle α, β, γ (deg.)94.040, 69.480, 90.040
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 10 through 325)
d_2ens_1(chain "B" and (resid 10 through 166 or resid 168...
d_1ens_2(chain "C" and (resid 48 through 89 or resid 106 through 327))
d_2ens_2(chain "D" and (resid 48 through 89 or resid 106...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ALAALAPROPROAA10 - 32510 - 325
d_21ens_1ALAALACYSCYSBB10 - 16610 - 166
d_22ens_1VALVALMETMETBB168 - 222168 - 222
d_23ens_1THRTHRLEULEUBB243 - 264243 - 264
d_24ens_1GLUGLUPROPROBB274 - 325274 - 325
d_11ens_2METMETASPASPCC48 - 8948 - 89
d_12ens_2GLUGLUARGARGCC106 - 327106 - 327
d_21ens_2METMETASPASPDD48 - 8948 - 89
d_22ens_2GLUGLUMETMETDD106 - 222106 - 222
d_23ens_2THRTHRALAALADD243 - 266243 - 266
d_24ens_2GLUGLUARGARGDD274 - 327274 - 327

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.99996984179511, -0.0028248816709185, 0.00723433091634), (-0.002847252809316, -0.99999119123164, 0.0030839277813129), (0.0072255554597309, -0.0031044327446121, -0.99996907644468)29.621685927883, -31.72919903582, 15.213614725681
2given(0.99712918900299, -0.075143695948472, -0.0093169414208679), (-0.07503030542519, -0.99710934400467, 0.011975364978803), (-0.010189882533131, -0.011241933008893, -0.99988488599247)28.352377154307, -31.604124585081, 14.711474116708

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
prenyltransferase


Mass: 36195.285 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. KS84 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 220 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-FPS / S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE / FARNESYL THIOPYROPHOSPHATE


Mass: 398.392 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H28O6P2S
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris, pH 5.5, 0.2 M Ammonium sulfate, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.045 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 31, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.045 Å / Relative weight: 1
Reflection twinOperator: h,-k,-h-l / Fraction: 0.5
ReflectionResolution: 2→50 Å / Num. obs: 86258 / % possible obs: 97.6 % / Redundancy: 3.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Net I/σ(I): 12.71
Reflection shellResolution: 2→2.12 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 1.75 / Num. unique obs: 13824 / CC1/2: 0.746 / % possible all: 96.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2.4158refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9V4G

9v4g


Resolution: 2→44.53 Å / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 30.4056
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2722 4203 4.87 %
Rwork0.2382 82052 -
obs0.2412 86255 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.67 Å2
Refinement stepCycle: LAST / Resolution: 2→44.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8078 0 57 210 8345
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00778255
X-RAY DIFFRACTIONf_angle_d1.051111168
X-RAY DIFFRACTIONf_chiral_restr0.05261270
X-RAY DIFFRACTIONf_plane_restr0.00851464
X-RAY DIFFRACTIONf_dihedral_angle_d14.69623023
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.0174527099856
ens_2d_2CCX-RAY DIFFRACTIONTorsion NCS1.4988436873547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.32492400.31994027X-RAY DIFFRACTION91.11
2.03-2.070.3271870.32624059X-RAY DIFFRACTION92.42
2.07-2.110.29641680.31384127X-RAY DIFFRACTION92.93
2.11-2.150.29312060.30474066X-RAY DIFFRACTION92.33
2.15-2.20.33061920.27574104X-RAY DIFFRACTION92.62
2.2-2.250.29632060.26764072X-RAY DIFFRACTION92.46
2.25-2.310.29262020.26954064X-RAY DIFFRACTION92.64
2.31-2.370.32832110.27054122X-RAY DIFFRACTION92.71
2.37-2.440.29962230.25954059X-RAY DIFFRACTION92.4
2.44-2.520.26311970.26754108X-RAY DIFFRACTION93
2.52-2.610.3361980.2584121X-RAY DIFFRACTION92.96
2.61-2.710.31062300.2614066X-RAY DIFFRACTION92.41
2.71-2.840.24742030.24434127X-RAY DIFFRACTION93.1
2.84-2.990.28441910.24834131X-RAY DIFFRACTION93.97
2.99-3.170.30511840.2534164X-RAY DIFFRACTION94.31
3.17-3.420.26922290.24384107X-RAY DIFFRACTION93.43
3.42-3.760.26222260.22594139X-RAY DIFFRACTION93.6
3.76-4.310.25732510.21044114X-RAY DIFFRACTION93.14
4.31-5.420.24551870.20364206X-RAY DIFFRACTION94.73
5.43-44.530.24792150.23184126X-RAY DIFFRACTION93.48
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)
10.582392129143540.258439469071690.103493510129291.09177634121660.430936844548840.42785116176465-0.00467826191581360.0158362333589950.182824029844630.0140890450294840.019723244161978-0.12028577612973-0.0225510190095550.052738076176423-0.00188851908237880.26468858612657-0.0247220509308290.0149591718653650.41972639905849-0.0581618081437970.285114565049720.898137648518030.553157317557320.67460125260315
20.45746690227541-0.19986852219828-0.174425192758021.14903718587520.274915566618910.563340595767490.0094574940160924-0.014050053129304-0.14695171644991-0.0674222515442420.030626527798776-0.137692856101190.0398243842328250.128578636430180.000819218391913390.266890829347230.0111761210302840.0112576853329060.45129347033249-0.0812255358727610.2943919488997531.821260098781-32.6134535912514.974080735706
30.288301137104520.044354263768507-0.202830127293380.765940188315550.349198310085871.04937119476320.127181760367610.16586897523479-0.211845829978050.0090520792276849-0.20579438660698-0.0885560384524850.27866958791541-0.12370960226657-0.0243150290155470.431761531165620.0100865826289090.00499154652232820.66067981905065-0.150187729861630.32525150945897-3.1847704829284-26.602188070793-22.677804545574
40.23851168761495-0.0807452086868050.230983379136270.919836021951380.243365212789271.15141786149320.075553872296415-0.239095394496260.156073036586160.07850404775037-0.089044036712274-0.18383824750928-0.25614469069084-0.20043647908317-0.0238406874098450.39898635598775-0.0268729320734990.0469049600827460.66150138907837-0.116061571821420.3268516857334927.835488090624-5.100837753879638.547681131673
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resseq 5:401)AA5 - 3251 - 283
22(chain B and resseq 10:402)BB10 - 3301 - 297
33(chain C and resseq 47:401)CC47 - 3271 - 240
44(chain D and resseq 40:402)DD40 - 3341 - 259

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