Cryo-EM Structure of the Class II Cyclase Domain in the Bifunctional Copalyl Diphosphate Synthase from Penicillium verruculosum

Method: ELECTRON MICROSCOPY D_max: 82.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q3i
deposition_date	2025-08-18
last_revision	2025-09-24
title	Cryo-EM Structure of the Class II Cyclase Domain in the Bifunctional Copalyl Diphosphate Synthase from Penicillium verruculosum
keywords	Terpene, Natural products, Cyclization, LYASE; LYASE
method	ELECTRON MICROSCOPY

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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	24.46 Å
rg_electron	23.45 Å
i0	41730300.00
molecular_weight	51395.0 kDa
excluded_volume	64716 Å³
envelope_volume	74199 Å³
shell_volume	26371 Å³
envelope_diameter	83.8 Å
shell_rg	30.57 Å
envelope_rg	23.58 Å
shape_rg	23.45 Å
total_rg	24.28 Å
total_atoms	3635
n_residues	494
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	82.5 Å
rg_real	24.43 Å
rg_real_error	0.49 Å
i0_real	4.1730e+07
i0_real_error	5.6260e+05
rg_reciprocal	24.44 Å
i0_reciprocal	41730000.0000
total_estimate	0.8829
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	27.5 Å
skewness	0.317
kurtosis	-0.387
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	14280000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.839; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.995

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4. Crystallography & Experiment

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5. Entities & Polymer Info (1)

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.900 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.90 Å
resolution_method	—
num_particles	381049

description	Copalyl diphosphate synthase
formula_weight	110996.0 kDa
ec_number	5.5.1.12,2.5.1.29
src_method	man
entity_count	1

Cryo-EM Structure of the Class II Cyclase Domain in the Bifunctional Copalyl Diphosphate Synthase from Penicillium verruculosum

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

EM 3D

5. Entities & Polymer Info (1)

Entity 1 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Talaromyces verruculosus
ncbi_taxonomy_id	198730
host_organism	Escherichia coli BL21(DE3)

fit	/app/data/saxs_computation/q3/9q3i/9q3i.fit
pddf	/app/data/pr_computation/q3/9q3i/9q3i.pr.out
profile	/app/data/saxs_computation/q3/9q3i/9q3i.dat

type	polypeptide(L)
strand_id	A
atom_count	3635