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- PDB-9v4h: Prenyltransferase Ord1 Q216A-FSPP -

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Basic information

Entry
Database: PDB / ID: 9v4h
TitlePrenyltransferase Ord1 Q216A-FSPP
Componentsprenyltransferase
KeywordsTRANSFERASE / Prenyltransferase
Function / homologyChem-FPS
Function and homology information
Biological speciesStreptomyces sp. KS84 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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)145,3747
Polymers144,5534
Non-polymers8213
Water95553
1
A: prenyltransferase
D: prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6994
Polymers72,2762
Non-polymers4232
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: prenyltransferase
C: prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6753
Polymers72,2762
Non-polymers3981
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.930, 71.870, 84.000
Angle α, β, γ (deg.)86.280, 69.390, 89.990
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 7 through 89 or resid 96 through 325))
d_2ens_1(chain "B" and resid 7 through 325)
d_1ens_2(chain "C" and (resid 45 through 252 or resid 254 through 281 or resid 288 through 331))
d_2ens_2(chain "D" and (resid 45 through 224 or resid 239 through 331))

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_1PROPROASPASPAA7 - 897 - 89
d_12ens_1SERSERPROPROAA96 - 32596 - 325
d_21ens_1PROPROPROPROBB7 - 3257 - 325
d_11ens_2GLYGLYARGARGCC45 - 25245 - 252
d_12ens_2PROPROASPASPCC254 - 281254 - 281
d_13ens_2GLYGLYGLUGLUCC288 - 331288 - 331
d_21ens_2GLYGLYTYRTYRDD45 - 22445 - 224
d_22ens_2ASNASNGLUGLUDD239 - 331239 - 331

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.99999759886948, 0.0020825222097516, 0.00068217044705833), (0.0020860519398212, -0.99998422555199, -0.0052150776104281), (0.00067129917124679, 0.0052164881313305, -0.99998616870885)0.23151698504964, -38.956689865726, -92.366370757432
2given(0.99948111913032, 0.032105768769561, -0.0025907747320229), (0.032114205600632, -0.99947881278614, 0.0032833809162829), (-0.002484008984878, -0.0033648779051467, -0.99999125360977)0.39851151629333, -37.215196270531, -92.364603899839

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Components

#1: Protein
prenyltransferase


Mass: 36138.234 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: DDBJ LC876682 / Source: (gene. exp.) Streptomyces sp. KS84 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: 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.: 2 / Source method: obtained synthetically / Formula: C15H28O6P2S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
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: 44.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris, pH 5.5, 0.24 M Lithium sulfate, 15% 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: Dec 14, 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: 2.2→50 Å / Num. obs: 64136 / % possible obs: 97.9 % / Redundancy: 3.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Net I/σ(I): 11.37
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 10294 / CC1/2: 0.767 / % possible all: 97

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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: 2.2→44.26 Å / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 28.8567
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2534 3270 5.1 %
Rwork0.2357 60866 -
obs0.2379 64136 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.66 Å2
Refinement stepCycle: LAST / Resolution: 2.2→44.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8348 0 49 53 8450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00288531
X-RAY DIFFRACTIONf_angle_d0.645511562
X-RAY DIFFRACTIONf_chiral_restr0.03941318
X-RAY DIFFRACTIONf_plane_restr0.0051526
X-RAY DIFFRACTIONf_dihedral_angle_d14.07013139
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.93716901619265
ens_2d_2CCX-RAY DIFFRACTIONTorsion NCS1.8184232848052
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.30751580.30613015X-RAY DIFFRACTION91.64
2.24-2.280.30641620.30253065X-RAY DIFFRACTION92.01
2.28-2.320.32571570.28922994X-RAY DIFFRACTION92.84
2.32-2.370.28961570.29262979X-RAY DIFFRACTION91.92
2.37-2.420.31271620.29053077X-RAY DIFFRACTION93.27
2.42-2.480.28871600.2883047X-RAY DIFFRACTION92.42
2.48-2.540.31561600.27333036X-RAY DIFFRACTION92.96
2.54-2.610.30081590.27553018X-RAY DIFFRACTION92.89
2.61-2.680.29991590.27933011X-RAY DIFFRACTION92.59
2.68-2.770.29461600.27223056X-RAY DIFFRACTION93.51
2.77-2.870.27891600.25653035X-RAY DIFFRACTION92.9
2.87-2.980.28031620.24933077X-RAY DIFFRACTION93.13
2.98-3.120.2941610.25713051X-RAY DIFFRACTION92.88
3.12-3.280.28151600.25923052X-RAY DIFFRACTION93.3
3.28-3.490.26241610.24383055X-RAY DIFFRACTION93.83
3.49-3.760.22931600.22253048X-RAY DIFFRACTION94.05
3.76-4.140.21391620.20613075X-RAY DIFFRACTION93.98
4.14-4.740.20211630.18963087X-RAY DIFFRACTION94.14
4.74-5.960.25721630.2323109X-RAY DIFFRACTION94.07
5.97-44.260.22131610.20633042X-RAY DIFFRACTION93.48
Refinement TLS params.Method: refined / Origin x: -28.644289520492 Å / Origin y: -19.129890364581 Å / Origin z: -46.251960127798 Å
111213212223313233
T0.30561547376217 Å20.010104663492337 Å2-0.013042266507634 Å2-0.49695390714165 Å20.051738940679967 Å2--0.36713309945445 Å2
L0.0081672099053002 °20.031611401210288 °2-0.052113667455926 °2-0.1727874292248 °2-0.3666329490007 °2--1.2643972831093 °2
S0.01653019207242 Å °0.0019632538549314 Å °0.0097823573108242 Å °-0.019859573420452 Å °0.0018208761054634 Å °0.054252090969197 Å °0.038442618265052 Å °-0.050880073214722 Å °7.3415530586347E-5 Å °
Refinement TLS groupSelection details: all

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