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- PDB-9v3u: Crystal structure of the aromatic prenyltransferase AtaPT(M7) mut... -

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Basic information

Entry
Database: PDB / ID: 9v3u
TitleCrystal structure of the aromatic prenyltransferase AtaPT(M7) mutant from Aspergillus terreus in complex with GSPP
ComponentsAromatic prenyltransferase
KeywordsTRANSFERASE / aromatic prenyltransferase
Function / homologyAromatic prenyltransferase DMATS-type, fungi / Aromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase / transferase activity, transferring alkyl or aryl (other than methyl) groups / alkaloid metabolic process / GERANYL S-THIOLODIPHOSPHATE / PYROPHOSPHATE 2- / Aromatic prenyltransferase
Function and homology information
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.20000051852 Å
AuthorsHuang, H.S. / Zhang, Z.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Simultaneous Multi-Parameter Directed Evolution of the Prenyltransferase AtaPT: Developing a Facile Access to Diverse Rare C-prenylated Flavonoids
Authors: Huang, H.S. / Zhang, Z.M.
History
DepositionMay 22, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 27, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aromatic prenyltransferase
B: Aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9814
Polymers93,4752
Non-polymers5062
Water3,045169
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0682
Polymers46,7381
Non-polymers3301
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-4 kcal/mol
Surface area16380 Å2
MethodPISA
3
B: Aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9142
Polymers46,7381
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint1 kcal/mol
Surface area16820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.02, 96.45, 132.94
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-683-

HOH

21B-686-

HOH

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Components

#1: Protein Aromatic prenyltransferase


Mass: 46737.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus terreus (mold) / Gene: PT / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B0UHJ4
#2: Chemical ChemComp-GST / GERANYL S-THIOLODIPHOSPHATE / S-[(2E)-3,7-DIMETHYLOCTA-2,6-DIENYL] TRIHYDROGEN THIODIPHOSPHATE


Mass: 330.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C10H20O6P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 100 mM Bis-Tris Ph 6.5,200 mM (NH4)2SO4, 25% peg 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Nov 27, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.2→78.9261 Å / Num. obs: 45788 / % possible obs: 99.8 % / Redundancy: 13.3 % / CC1/2: 0.781 / Net I/σ(I): 3.3
Reflection shellResolution: 2.2→2.27 Å / Num. unique obs: 31866 / CC1/2: 0.781

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.20000051852→48.225 Å / SU ML: 0.273945893034 / Cross valid method: FREE R-VALUE / σ(F): 1.34352711765 / Phase error: 23.9614294143
RfactorNum. reflection% reflection
Rfree0.233772817078 2000 4.36795666987 %
Rwork0.193963812416 43788 -
obs0.195766349658 45788 99.9585216233 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.5377726046 Å2
Refinement stepCycle: LAST / Resolution: 2.20000051852→48.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6225 0 28 169 6422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003084428419616404
X-RAY DIFFRACTIONf_angle_d0.7391326734638718
X-RAY DIFFRACTIONf_chiral_restr0.0277050926534984
X-RAY DIFFRACTIONf_plane_restr0.003490960671721108
X-RAY DIFFRACTIONf_dihedral_angle_d12.58485869442331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.201-2.2550.323177477851400.2498594942773078X-RAY DIFFRACTION99.9689344517
2.255-2.3160.2960840013881410.2474680873733064X-RAY DIFFRACTION100
2.316-2.38410.338162223011410.2349909276493104X-RAY DIFFRACTION100
2.3841-2.46110.2802465106671410.2174670578283090X-RAY DIFFRACTION99.9690594059
2.4611-2.5490.3250131530761420.2282119991713105X-RAY DIFFRACTION100
2.549-2.65110.2580227100451410.2215017964643082X-RAY DIFFRACTION100
2.6511-2.77170.2740697380911410.223083862953095X-RAY DIFFRACTION100
2.7717-2.91790.2483819072721420.2201874648273098X-RAY DIFFRACTION99.907493062
2.9179-3.10060.2789322347421420.2185350997553115X-RAY DIFFRACTION100
3.1006-3.340.2365527720351420.2019235202963122X-RAY DIFFRACTION99.9693721286
3.34-3.6760.2171998890661440.1877916536513141X-RAY DIFFRACTION99.939154244
3.676-4.20760.2062142180051450.1661864361933162X-RAY DIFFRACTION100
4.2076-5.30010.1813877169171450.156621582883195X-RAY DIFFRACTION99.9700688417
5.3001-48.2250.2209557438531530.1894541406883337X-RAY DIFFRACTION99.7712978845
Refinement TLS params.Method: refined / Origin x: -115.594611048 Å / Origin y: 12.3519260911 Å / Origin z: 283.03159298 Å
111213212223313233
T0.278101193904 Å20.0700693058328 Å20.0125449509422 Å2-0.231369830467 Å2-0.0089454780899 Å2--0.250525671231 Å2
L0.843629289977 °20.277025892224 °2-0.120738449336 °2-0.927266872861 °20.201451565849 °2--1.03567529643 °2
S-0.0332307200714 Å °-0.112877749167 Å °0.047957834541 Å °0.156963844588 Å °0.063387564885 Å °0.0558716131508 Å °-0.1201360753 Å °-0.0239450758715 Å °-0.033880068583 Å °
Refinement TLS groupSelection details: all

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