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- PDB-9v5f: Crystal structure of the aromatic prenyltransferase AtaPT(G326W) ... -

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Basic information

Entry
Database: PDB / ID: 9v5f
TitleCrystal structure of the aromatic prenyltransferase AtaPT(G326W) mutant from Aspergillus terreus
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 / Aromatic prenyltransferase
Function and homology information
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69798139109 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 25, 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


Theoretical massNumber of molelcules
Total (without water)93,2272
Polymers93,2272
Non-polymers00
Water54030
1
A: Aromatic prenyltransferase

A: Aromatic prenyltransferase


Theoretical massNumber of molelcules
Total (without water)93,2272
Polymers93,2272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_855-x+3,-y,z1
Buried area1650 Å2
ΔGint-12 kcal/mol
Surface area31650 Å2
MethodPISA
2
B: Aromatic prenyltransferase

B: Aromatic prenyltransferase


Theoretical massNumber of molelcules
Total (without water)93,2272
Polymers93,2272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_855-x+3,-y,z1
Buried area1650 Å2
ΔGint-12 kcal/mol
Surface area31610 Å2
MethodPISA
3
A: Aromatic prenyltransferase
B: Aromatic prenyltransferase

A: Aromatic prenyltransferase
B: Aromatic prenyltransferase


Theoretical massNumber of molelcules
Total (without water)186,4544
Polymers186,4544
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_855-x+3,-y,z1
Buried area11070 Å2
ΔGint-27 kcal/mol
Surface area55480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.772, 137.388, 69.762
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
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

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Components

#1: Protein Aromatic prenyltransferase


Mass: 46613.477 Da / Num. of mol.: 2 / Mutation: G326W
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
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: 2.46 Å3/Da / Density % sol: 50.03 %
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 28, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.69→68.694 Å / Num. obs: 25024 / % possible obs: 96.1 % / Redundancy: 12.8 % / CC1/2: 0.845 / Net I/σ(I): 2.4
Reflection shellResolution: 2.7→2.84 Å / Num. unique obs: 25024 / CC1/2: 0.845

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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: 2.69798139109→68.694 Å / SU ML: 0.321334768585 / Cross valid method: NONE / σ(F): 1.32736365493 / Phase error: 25.639232006
RfactorNum. reflection% reflection
Rfree0.245730836869 1982 7.99129102492 %
Rwork0.209455864039 22820 -
obs0.212345839871 24802 95.2421181982 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.8430887088 Å2
Refinement stepCycle: LAST / Resolution: 2.69798139109→68.694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6256 0 0 30 6286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002907124102526420
X-RAY DIFFRACTIONf_angle_d0.7026192241128758
X-RAY DIFFRACTIONf_chiral_restr0.0261786044217989
X-RAY DIFFRACTIONf_plane_restr0.003677578591511121
X-RAY DIFFRACTIONf_dihedral_angle_d11.99188669092322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.698-2.76550.3076057576311450.2582310865031669X-RAY DIFFRACTION100
2.7655-2.84020.3341240661461470.2630134950261688X-RAY DIFFRACTION99.9455337691
2.8402-2.92380.2908473424211460.2556367747471685X-RAY DIFFRACTION100
2.9238-3.01820.2996934448871460.2819025689191673X-RAY DIFFRACTION99.3989071038
3.0182-3.1260.3094024855621440.2820713890131666X-RAY DIFFRACTION99.2868897422
3.126-3.25120.3157390845371410.2729155395691642X-RAY DIFFRACTION97.378481704
3.2512-3.39920.3515899587761380.2815784621561623X-RAY DIFFRACTION95.2406706328
3.3992-3.57840.2607362386821030.2320150123031158X-RAY DIFFRACTION67.7592692101
3.5784-3.80260.2469915152671250.2222499457241430X-RAY DIFFRACTION84.6949891068
3.8026-4.09610.2184285196541360.1970066482191545X-RAY DIFFRACTION90.0857449089
4.0961-4.50830.2048430852191470.176411512221702X-RAY DIFFRACTION100
4.5083-5.16040.1998761149231520.1661671090811745X-RAY DIFFRACTION100
5.1604-6.50080.2194352089811520.1865425253231751X-RAY DIFFRACTION99.9474789916
6.5008-68.690.2284746883891600.1861030370061843X-RAY DIFFRACTION99.4538232373
Refinement TLS params.Method: refined / Origin x: 131.591997348 Å / Origin y: 17.8300029035 Å / Origin z: 82.4117629553 Å
111213212223313233
T0.309730303082 Å2-0.00465941396823 Å20.0738162988036 Å2-0.344031345576 Å2-0.0317615910825 Å2--0.395576570618 Å2
L1.34903264823 °2-0.794299384517 °20.363561003016 °2-1.77236139948 °20.03207359383 °2--0.942496938865 °2
S0.131493694815 Å °-0.0966630355414 Å °0.215385596496 Å °-0.0679289880967 Å °-0.0355024112722 Å °0.120074260775 Å °-0.00388653272818 Å °-0.0575826588995 Å °-0.0697062202645 Å °
Refinement TLS groupSelection details: all

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