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9v5g

Crystal structure of the aromatic prenyltransferase AtaPT(M8) mutant from Aspergillus terreus in complex with DMSPP and KMP

Method: X-RAY DIFFRACTION D_max: 99.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9v5g
deposition_date	2025-05-25
last_revision	2026-05-27
title	Crystal structure of the aromatic prenyltransferase AtaPT(M8) mutant from Aspergillus terreus in complex with DMSPP and KMP
keywords	aromatic prenyltransferase, TRANSFERASE; TRANSFERASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	30.14 Å
rg_electron	29.37 Å
i0	118471000.00
molecular_weight	89601.0 kDa
excluded_volume	113430 Å³
envelope_volume	133540 Å³
shell_volume	38104 Å³
envelope_diameter	101.2 Å
shell_rg	36.58 Å
envelope_rg	29.36 Å
shape_rg	29.38 Å
total_rg	29.98 Å
total_atoms	6320
n_residues	793
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	99.6 Å
rg_real	30.19 Å
rg_real_error	0.48 Å
i0_real	1.1850e+08
i0_real_error	1.5990e+06
rg_reciprocal	30.17 Å
i0_reciprocal	118500000.0000
total_estimate	0.8775
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.8 Å
skewness	0.425
kurtosis	-0.321
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0002
highest_alpha	51590000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.836; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.910

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Aromatic prenyltransferase
formula_weight	47605.6 kDa
mutation	I167A/E169A/S170Q/C175M/S177A/L323Q/P324H/N328R
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	6416

MLPPSDSKDPRPWQILSQALGFPNYDQELWWQNTAETLNRVLEQCDYSVHLQYKYLAFYHKYILPSLGPFRRPGVEPEYISGLSHGGHPLEISVKIDKSKTICRLGLQAIGPLAGTARDPLNSFGDRELLKNLATLLPHVDLRLFDHFNAQVGLDRAQCAVATTKLAKAQHNIVMTALDLKDGEVIPKVYFSTIPKGLVTETPLFDLTFAAIEQMEVYHKDAPLRTALSSLKDFLRPRVPTDASITPPLTGLIGVDCIDPMLSRLKVYLATFRMDLSLIRDYWTLGGLLTDAGTMKGLEMVETLAKTLKLGDEACETLDAERQHFGIRYAMKPGTAELAPPQIYFPLLGINDGFIADALVEFFQYMGWEDQANRYKDELKAKFPNVDISQTKNVHRWLGVAYSETKGPSMNIYYDVVAGNVARV

Source

organism	Aspergillus terreus
ncbi_taxonomy_id	33178
host_organism	Escherichia coli

Entity 2 non-polymer

description	DIMETHYLALLYL S-THIOLODIPHOSPHATE
formula_weight	262.2 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	3,5,7-TRIHYDROXY-2-(4-HYDROXYPHENYL)-4H-CHROMEN-4-ONE
formula_weight	286.2 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	96

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6. Citations (1)

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length_a	71.710 Å
length_b	95.590 Å
length_c	137.958 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 2 21 21
int_tables_number	18
crystal_system	orthorhombic

resolution	2.500 Å
resolution_low	44.105 Å
r_factor	0.2082
r_work	0.2053
r_free	0.2520

fit	/app/data/saxs_computation/v5/9v5g/9v5g.fit
pddf	/app/data/pr_computation/v5/9v5g/9v5g.pr.out
profile	/app/data/saxs_computation/v5/9v5g/9v5g.dat

Crystal structure of the aromatic prenyltransferase AtaPT(M8) mutant from Aspergillus terreus in complex with DMSPP and KMP

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction