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- PDB-9v4g: Prenyltransferase Ord1 wild type -

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Basic information

Entry
Database: PDB / ID: 9v4g
TitlePrenyltransferase Ord1 wild type
Componentsprenyltransferase
KeywordsTRANSFERASE / Prenyltransferase
Biological speciesStreptomyces sp. KS84 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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
C: prenyltransferase
D: prenyltransferase
B: prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,38012
Polymers144,7814
Non-polymers5998
Water3,117173
1
A: prenyltransferase
B: prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7076
Polymers72,3912
Non-polymers3164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: prenyltransferase
D: prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,6736
Polymers72,3912
Non-polymers2824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.000, 72.210, 84.190
Angle α, β, γ (deg.)86.040, 69.500, 90.020
Int Tables number1
Space group name H-MP1
Space group name HallP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 8 through 90 or resid 97 through 330))
d_2ens_1chain "C"
d_1ens_2(chain "B" and (resid 44 through 224 or resid 240 through 328))
d_2ens_2(chain "D" and (resid 44 through 90 or resid 104...

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_1GLNGLNLEULEUCB8 - 3308 - 330
d_11ens_2PHEPHETYRTYRBD44 - 22444 - 224
d_12ens_2GLYGLYLEULEUBD240 - 328240 - 328
d_21ens_2PHEPHECYSCYSDC44 - 9044 - 90
d_22ens_2PHEPHETYRTYRDC104 - 224104 - 224
d_23ens_2GLYGLYALAALADC226 - 266226 - 266
d_24ens_2ALAALAARGARGDC273 - 275273 - 275
d_25ens_2LYSLYSLEULEUDC277 - 328277 - 328

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.99997968608225, -0.00096702332452842, 0.0063001816429663), (-0.00096430197164901, -0.99999944046052, -0.00043497167191598), (0.0063005987455182, 0.00042888755835716, -0.99998005905663)0.57187657639924, -39.271909935581, -92.772870236911
2given(0.99747701070139, 0.070572669376789, 0.0076883977039424), (0.0705695394455, -0.99750663178962, 0.000677966199635), (0.0077170735819742, -0.00013368901312744, -0.99997021400769)2.0990144419089, -36.651776024055, -92.326056465626

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Components

#1: Protein
prenyltransferase


Mass: 36195.285 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-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.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.21 Å3/Da / Density % sol: 44.4 %
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-1A / Wavelength: 1.045 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 30, 2021
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.045 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 74272 / % possible obs: 97.6 % / Redundancy: 3.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.063 / Net I/σ(I): 10.58
Reflection shellResolution: 2.1→2.22 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 2.25 / Num. unique obs: 11833 / CC1/2: 0.774 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX1.19.2.4158refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Initial phase from Se-SAD model

Resolution: 2.1→44.4 Å / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 28.0116
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2459 3795 5.12 %
Rwork0.2287 70359 -
obs0.2324 74154 97.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.5 Å2
Refinement stepCycle: LAST / Resolution: 2.1→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8506 0 35 173 8714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00378676
X-RAY DIFFRACTIONf_angle_d0.675311748
X-RAY DIFFRACTIONf_chiral_restr0.03981332
X-RAY DIFFRACTIONf_plane_restr0.00571550
X-RAY DIFFRACTIONf_dihedral_angle_d13.81643173
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS1.4381033974965
ens_2d_2DBX-RAY DIFFRACTIONTorsion NCS2.3339470374973
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.29981760.30543343X-RAY DIFFRACTION88.96
2.13-2.170.28831860.29263534X-RAY DIFFRACTION92.15
2.17-2.210.31421840.29793502X-RAY DIFFRACTION92.28
2.21-2.260.27991880.28693564X-RAY DIFFRACTION92.43
2.26-2.310.31161800.28193435X-RAY DIFFRACTION92.56
2.31-2.360.30421890.27963580X-RAY DIFFRACTION92.6
2.36-2.420.26851850.26753509X-RAY DIFFRACTION92.76
2.42-2.490.27131860.26993549X-RAY DIFFRACTION92.71
2.49-2.560.27481860.25713520X-RAY DIFFRACTION92.9
2.56-2.640.26691840.2553505X-RAY DIFFRACTION93.17
2.64-2.740.29851880.26283578X-RAY DIFFRACTION93.13
2.74-2.850.27671850.24573514X-RAY DIFFRACTION93.23
2.85-2.980.29411870.24783542X-RAY DIFFRACTION93.21
2.98-3.130.2811890.25623590X-RAY DIFFRACTION93.47
3.13-3.330.25311840.24343501X-RAY DIFFRACTION93.36
3.33-3.590.27871890.22483581X-RAY DIFFRACTION93.43
3.59-3.950.21491850.20993532X-RAY DIFFRACTION92.7
3.95-4.520.21371860.18443531X-RAY DIFFRACTION93.26
4.52-5.690.21011860.20683530X-RAY DIFFRACTION93.07
5.69-44.40.2181850.20733506X-RAY DIFFRACTION91.95
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)
10.39130186143458-0.29173707857172-0.0388944265972641.207922170986-0.284161428872490.42832971636640.050007888304569-0.0160307593863050.18560506239097-0.028780705973109-0.000111009907976820.17215578004827-0.020669912783647-0.0651286578656240.000307777165309620.29670361093029-6.5700882608287E-6-0.00620994847389060.41525497555380.0520098266624590.32199564974716-31.007058620554-6.0428455639027-78.79376463537
20.030703418963335-0.0119452346952670.330218616504011.153375024426-0.0157682316764751.96093454561090.16790951367695-0.1736212646452-0.13376076739490.19598316643228-0.13887847733480.16092012801380.584656980383180.12976315605689-0.000494891168324270.52697293856455-0.010018164364329-0.00966611746076520.572081624297470.135600996885150.34109329497631-25.840358865058-32.738598763987-54.718770273487
3-0.0385113149211040.54936661170795-0.0956819509423591.0717338555573-0.425928694841450.7559778099485-0.0546438910737580.10387280010394-0.13877989685811-0.0200480569976160.124827229489510.181121007089550.10657184471452-0.192481543690640.000843824359366790.28416678544837-0.0116334861609870.0076891635436580.422775146459380.0711547616087480.39021385096902-31.305002754713-35.599149306714-15.42182326993
40.28041806465575-0.13211067950864-0.071114967527190.328476787198190.128837351509251.45858320443270.0598362599161490.234340011964550.22430161662132-0.069904938302804-0.0536046421985050.11533008252802-0.32253663825320.023798195336043-0.000305281786281860.46241342804528-0.00356717567636180.00165892857719360.665900665907820.15793970791790.38384510968211-27.084507106076-5.6903672680097-37.272195349617
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 5:403)AA5 - 3301 - 313
22(chain B and resseq 8:406)BD39 - 3341 - 262
33(chain C and resseq 44:330)CB44 - 33037 - 304
44(chain D and resseq 39:403)DC44 - 3281 - 259

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