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9rd2

Crystal structure of a leaf-branch compost cutinase variant (LCC_ICCG)

Method: X-RAY DIFFRACTION D_max: 55.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rd2
deposition_date	2025-05-30
last_revision	2026-06-10
title	Crystal structure of a leaf-branch compost cutinase variant (LCC_ICCG)
keywords	PETase, PET-degrading, HYDROLASE; HYDROLASE
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	17.88 Å
rg_electron	16.56 Å
i0	14383300.00
molecular_weight	27860.0 kDa
excluded_volume	34503 Å³
envelope_volume	36824 Å³
shell_volume	18116 Å³
envelope_diameter	54.6 Å
shell_rg	23.23 Å
envelope_rg	16.79 Å
shape_rg	16.55 Å
total_rg	17.53 Å
total_atoms	3879
n_residues	257
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	55.7 Å
rg_real	17.70 Å
rg_real_error	0.22 Å
i0_real	1.4380e+07
i0_real_error	1.4990e+05
rg_reciprocal	17.73 Å
i0_reciprocal	14380000.0000
total_estimate	0.8903
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.1 Å
skewness	0.023
kurtosis	-0.510
angular_range	— – 0.4450 Å⁻¹
current_alpha	0.0000
highest_alpha	4617000.0000
n_real_points	75
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.999

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Leaf-branch compost cutinase
formula_weight	28866.3 kDa
ec_number	3.1.1.74,3.1.1.101
mutation	Y93G, D204C, F209I, S249C
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4061

MSNPYQRGPNPTRSALTADGPFSVATYTVSRLSVSGFGGGVIYYPTGTSLTFGGIAMSPGYTADASSLAWLGRRLASHGFVVLVINTNSRFDGPDSRASQLSAALNYLRTSSPSAVRARLDANRLAVAGHSMGGGGTLRIAEQNPSLKAAVPLTPWHTDKTFNTSVPVLIVGAEADTVAPVSQHAIPFYQNLPSTTPKVYVELCNASHIAPNSNNAAISVYTISWMKLWVDNDTRYRQFLCNVNDPALCDFRTNNRHCQLEHHHHHH

Source

organism	unidentified prokaryotic organism
ncbi_taxonomy_id	2725
host_organism	Escherichia coli

Entity 2 non-polymer

description	IMIDAZOLE
formula_weight	69.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	NITRATE ION
formula_weight	62.0 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	113

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6. Citations (1)

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length_a	88.081 Å
length_b	88.081 Å
length_c	73.738 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 41 21 2
int_tables_number	92
crystal_system	—

resolution	1.640 Å
resolution_low	47.626 Å
r_factor	—
r_work	0.1706
r_free	0.2117

fit	/app/data/saxs_computation/rd/9rd2/9rd2.fit
pddf	/app/data/pr_computation/rd/9rd2/9rd2.pr.out
profile	/app/data/saxs_computation/rd/9rd2/9rd2.dat