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9rc3

Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 co-crystallized with Silver Nitrate

Method: X-RAY DIFFRACTION D_max: 105.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rc3
deposition_date	2025-05-27
title	Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 co-crystallized with Silver Nitrate
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	31.02 Å
rg_electron	30.96 Å
i0	175110000.00
molecular_weight	104160.0 kDa
excluded_volume	129230 Å³
envelope_volume	153980 Å³
shell_volume	41289 Å³
envelope_diameter	113.1 Å
shell_rg	38.15 Å
envelope_rg	31.33 Å
shape_rg	31.02 Å
total_rg	31.31 Å
total_atoms	7323
n_residues	922
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	105.4 Å
rg_real	31.12 Å
rg_real_error	0.87 Å
i0_real	1.7510e+08
i0_real_error	2.7860e+06
rg_reciprocal	31.08 Å
i0_reciprocal	175100000.0000
total_estimate	0.8612
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.1 Å
skewness	0.475
kurtosis	-0.232
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	59900000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.772; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.934; Smooth: 0.940

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Multicopper oxidase, type 2
formula_weight	59853.5 kDa
ec_number	1.-.-.-
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7347

MGSSHHHHHHSSGLVPRGSHMASMKNYTDYFFDEPAFDLHDGGYVPLEVSDAPEKPLNVPPLLKPDKETATDVYYTVTAEAGETQLLPGAKTKTWGYNTSLLGQTIVYRRGQHTHVTLKNTLPELTTFHWHGANVSGPYVDGGCHAPVYPGESKHIDFTLEQPATTLWLHAHPCPSTAEQVWHGLAAMVIVKDDHEASLPLPRNYGVDDIPVILQDRRFHENNQWDYRADYDPDGVAGPTAMINGTINPYFDVTTQKVRLRFLNGANRREWRLHFADDLPFTQIGGDGSLLPEPVKFTHLMLTCAERAEVIVDFGQYHEGDEVTLYTDDVPLLKFRIHAFKPDQTTLPDKLFDVKAPVVDPALPVRHVVMQGMDEGVAIDGKKFAMQRIDATQPIGKAQYWDVTNSNDAPGMVHPFHVHGTQFLVLSRNGHAPYPNEHGFKDTIGVNPGETVRLLVRFDLPGVYMYHCHIIEHEDGGMMAQIETFDPAKPKQEYKLMDMDTLMMALAKERGVKPSEIWMGGMQSYEKMGMKM

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	SILVER ION
formula_weight	107.9 kDa
src_method	nat
entity_count	2

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	19

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6. Citations (2)

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length_a	121.122 Å
length_b	121.122 Å
length_c	174.556 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	2.700 Å
resolution_low	104.890 Å
r_factor	0.2038
r_work	0.2015
r_free	0.2493

fit	/app/data/saxs_computation/rc/9rc3/9rc3.fit
pddf	/app/data/pr_computation/rc/9rc3/9rc3.pr.out
profile	/app/data/saxs_computation/rc/9rc3/9rc3.dat