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9rc8

Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 deletion 482-509 co-crystallized with Copper Chloride

Method: X-RAY DIFFRACTION D_max: 105.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rc8
deposition_date	2025-05-27
title	Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 deletion 482-509 co-crystallized with Copper Chloride
keywords	Laccase, oxidoreductase, multicopper oxidase; OXIDOREDUCTASE
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	31.04 Å
rg_electron	30.90 Å
i0	171677000.00
molecular_weight	103500.0 kDa
excluded_volume	128600 Å³
envelope_volume	153170 Å³
shell_volume	41162 Å³
envelope_diameter	113.2 Å
shell_rg	38.01 Å
envelope_rg	31.30 Å
shape_rg	30.96 Å
total_rg	31.26 Å
total_atoms	7296
n_residues	924
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	105.2 Å
rg_real	31.14 Å
rg_real_error	0.67 Å
i0_real	1.7170e+08
i0_real_error	2.5240e+06
rg_reciprocal	31.10 Å
i0_reciprocal	171700000.0000
total_estimate	0.8621
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	33.0 Å
skewness	0.478
kurtosis	-0.242
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0001
highest_alpha	68300000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.774; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.933; Smooth: 0.950

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Multicopper oxidase domain-containing protein
formula_weight	56560.5 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C
atom_count	7377

MGSSHHHHHHSSGLVPRGSHMASMKNYTDYFFDEPAFDLHDGGYVPLEVSDAPEKPLNVPPLLKPDKETATDVYYTVTAEAGETQLLPGAKTKTWGYNTSLLGQTIVYRRGQHTHVTLKNTLPELTTFHWHGANVSGPYVDGGCHAPVYPGESKHIDFTLEQPATTLWLHAHPCPSTAEQVWHGLAAMVIVKDDHEASLPLPRNYGVDDIPVILQDRRFHENNQWDYRADYDPDGVAGPTAMINGTINPYFDVTTQKVRLRFLNGANRREWRLHFADDLPFTQIGGDGSLLPEPVKFTHLMLTCAERAEVIVDFGQYHEGDEVTLYTDDVPLLKFRIHAFKPDQTTLPDKLFDVKAPVVDPALPVRHVVMQGMDEGVAIDGKKFAMQRIDATQPIGKAQYWDVTNSNDAPGMVHPFHVHGTQFLVLSRNGHAPYPNEHGFKDTIGVNPGETVRLLVRFDLPGVYMYHCHIIEHEDGGMMAQIETFDPAKPKQEYKLMDMDTLM

Source

organism	Pediococcus pentosaceus
ncbi_taxonomy_id	1255
host_organism	Escherichia coli K-12

Entity 2 non-polymer

description	COPPER (II) ION
formula_weight	63.5 kDa
src_method	syn
entity_count	8

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	81

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6. Citations (2)

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length_a	124.363 Å
length_b	124.363 Å
length_c	182.238 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 32 2 1
int_tables_number	154
crystal_system	—

resolution	3.200 Å
resolution_low	107.700 Å
r_factor	0.1619
r_work	0.1594
r_free	0.2098

fit	/app/data/saxs_computation/rc/9rc8/9rc8.fit
pddf	/app/data/pr_computation/rc/9rc8/9rc8.pr.out
profile	/app/data/saxs_computation/rc/9rc8/9rc8.dat

Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 deletion 482-509 co-crystallized with Copper Chloride

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