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9rc6

Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 mutant Y471L co-crystallized with Copper Chloride

Method: X-RAY DIFFRACTION D_max: 104.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rc6
deposition_date	2025-05-27
title	Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 mutant Y471L 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	31.14 Å
rg_electron	31.00 Å
i0	181370000.00
molecular_weight	105340.0 kDa
excluded_volume	130440 Å³
envelope_volume	155720 Å³
shell_volume	41633 Å³
envelope_diameter	112.2 Å
shell_rg	38.16 Å
envelope_rg	31.37 Å
shape_rg	31.06 Å
total_rg	31.38 Å
total_atoms	7411
n_residues	929
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	104.8 Å
rg_real	31.24 Å
rg_real_error	0.79 Å
i0_real	1.8140e+08
i0_real_error	2.9750e+06
rg_reciprocal	31.20 Å
i0_reciprocal	181400000.0000
total_estimate	0.8579
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	32.9 Å
skewness	0.472
kurtosis	-0.248
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	68380000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.784; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.944; Smooth: 0.852

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Multicopper oxidase domain-containing protein
formula_weight	59761.4 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,C,G
atom_count	7491

MGSSHHHHHHSSGLVPRGSHMASMKNYTDYFFDEPAFDLHDGGYVPLEVSDAPEKPLNVPPLLKPDKETATDVYYTVTAEAGETQLLPGAKTKTWGYNTSLLGQTIVYRRGQHTHVTLKNTLPELTTFHWHGANVSGPYVDGGCHAPVYPGESKHIDFTLEQPATTLWLHAHPCPSTAEQVWHGLAAMVIVKDDHEASLPLPRNYGVDDIPVILQDRRFHENNQWDYRADYDPDGVAGPTAMINGTINPYFDVTTQKVRLRFLNGANRREWRLHFADDLPFTQIGGDGSLLPEPVKFTHLMLTCAERAEVIVDFGQYHEGDEVTLYTDDVPLLKFRIHAFKPDQTTLPDKLFDVKAPVVDPALPVRHVVMQGMDEGVAIDGKKFAMQRIDATQPIGKAQYWDVTNSNDAPGMVHPFHVHGTQFLVLSRNGHAPYPNEHGFKDTIGVNPGETVRLLVRFDLPGVYMYHCHIIEHEDGGMMAQIETFDPAKPKQEAKLMDMDTLMMALAKERGVKPSEIWMGGMQSYEKMGMKM

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 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	8

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	64

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6. Citations (2)

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length_a	123.680 Å
length_b	123.680 Å
length_c	181.770 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	18

space_group	P 32 2 1
int_tables_number	154
crystal_system	—

resolution	2.600 Å
resolution_low	107.110 Å
r_factor	0.1913
r_work	0.1893
r_free	0.2286

fit	/app/data/saxs_computation/rc/9rc6/9rc6.fit
pddf	/app/data/pr_computation/rc/9rc6/9rc6.pr.out
profile	/app/data/saxs_computation/rc/9rc6/9rc6.dat

Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 mutant Y471L 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