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- PDB-9v4i: Prenyltransferase Ord1 D219A -

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Basic information

Entry
Database: PDB / ID: 9v4i
TitlePrenyltransferase Ord1 D219A
Componentsprenyltransferase
KeywordsTRANSFERASE / Prenyltransferase
Biological speciesStreptomyces sp. KS84 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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
Revision 1.1Oct 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)144,6295
Polymers144,6054
Non-polymers241
Water1448
1
A: prenyltransferase
D: prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3273
Polymers72,3032
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: prenyltransferase
C: prenyltransferase


Theoretical massNumber of molelcules
Total (without water)72,3032
Polymers72,3032
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.879, 72.425, 83.774
Angle α, β, γ (deg.)93.455, 110.501, 90.085
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 8 through 90 or resid 97 through 330))
d_2ens_1(chain "B" and (resid 8 through 225 or resid 239 through 330))
d_1ens_2(chain "C" and (resid 44 through 90 or resid 104...
d_2ens_2(chain "D" and (resid 44 through 224 or resid 240 through 330))

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_1GLNGLNCYSCYSAA8 - 908 - 90
d_12ens_1LYSLYSLEULEUAA97 - 33097 - 330
d_21ens_1GLNGLNASPASPBB8 - 2258 - 225
d_22ens_1ASNASNLEULEUBB239 - 330239 - 330
d_11ens_2PHEPHECYSCYSCC44 - 9044 - 90
d_12ens_2PHEPHETYRTYRCC104 - 224104 - 224
d_13ens_2GLYGLYALAALACC226 - 266226 - 266
d_14ens_2ALAALAARGARGCC270 - 275270 - 275
d_15ens_2LYSLYSLEULEUCC277 - 330277 - 330
d_21ens_2PHEPHETYRTYRDD44 - 22444 - 224
d_22ens_2GLYGLYLEULEUDD240 - 330240 - 330

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.99996676584327, -0.003739223764043, -0.0072446818138963), (-0.0037339070944541, -0.99999274974474, 0.00074725883824448), (-0.0072474234561097, -0.00072018303490516, -0.99997347774311)-0.020995093375304, 25.21102681201, 63.37820832991
2given(0.99785080469281, 0.065051248114615, -0.0078807799516653), (0.065032748550188, -0.99787979071684, -0.0025816457782098), (-0.0080320103289156, 0.0020635885362424, -0.999965613615)-0.16629129403154, 24.905435216156, 63.748281114294

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Components

#1: Protein
prenyltransferase


Mass: 36151.277 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-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.2 Å3/Da / Density % sol: 44.2 %
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% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2023
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
Reflection twinOperator: h,-k,h-l / Fraction: 0.5
ReflectionResolution: 2.8→50 Å / Num. obs: 31241 / % possible obs: 97.8 % / Redundancy: 3.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.118 / Net I/σ(I): 11.83
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.712 / Mean I/σ(I) obs: 3.09 / Num. unique obs: 4990 / CC1/2: 0.771 / % possible all: 97.2

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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: 2.8→44.35 Å / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 26.8704
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2539 1588 5.08 %
Rwork0.224 29651 -
obs0.2307 31239 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.49 Å2
Refinement stepCycle: LAST / Resolution: 2.8→44.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8567 0 1 8 8576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00398714
X-RAY DIFFRACTIONf_angle_d0.724411810
X-RAY DIFFRACTIONf_chiral_restr0.04491343
X-RAY DIFFRACTIONf_plane_restr0.0061560
X-RAY DIFFRACTIONf_dihedral_angle_d15.47783186
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.4337696506821
ens_2d_2CCX-RAY DIFFRACTIONTorsion NCS2.3473918827843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.890.29531400.26412672X-RAY DIFFRACTION92.11
2.89-2.990.29181420.27562690X-RAY DIFFRACTION92.89
2.99-3.110.29631430.27132714X-RAY DIFFRACTION93.43
3.11-3.250.28471410.25752688X-RAY DIFFRACTION92.88
3.25-3.430.24071400.2482650X-RAY DIFFRACTION93.11
3.43-3.640.23351440.22962735X-RAY DIFFRACTION93.28
3.64-3.920.2331430.22072720X-RAY DIFFRACTION93.66
3.92-4.310.23811420.20562694X-RAY DIFFRACTION93.74
4.31-4.940.22221450.1962766X-RAY DIFFRACTION93.83
4.94-6.220.28181420.24092688X-RAY DIFFRACTION93.53
6.22-44.350.2831400.22232660X-RAY DIFFRACTION91.66
Refinement TLS params.Method: refined / Origin x: 0.53434265609733 Å / Origin y: 12.446420539981 Å / Origin z: 31.511070508197 Å
111213212223313233
T0.36447480095495 Å2-0.053641792138992 Å20.016240728317643 Å2-0.61183822032425 Å2-0.082410445313855 Å2--0.47437803418218 Å2
L-0.11346767076813 °2-0.049398267371967 °2-0.041441780905506 °2-0.14520876581168 °20.53022249818028 °2--1.5676410305347 °2
S0.0047280588584196 Å °-0.016044100592783 Å °-0.015433165370851 Å °-0.037675183433561 Å °0.014849297320962 Å °-0.05207759614502 Å °-0.10810530463663 Å °0.094400890492523 Å °4.966218248151E-5 Å °
Refinement TLS groupSelection details: all

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