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9rc5

;Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 mutant E451L co-crystallized with Silver Nitrate (1 molecule in assymetric unit) ;

Method: X-RAY DIFFRACTION D_max: 71.6 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rc5
deposition_date	2025-05-27
title	;Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 mutant E451L co-crystallized with Silver Nitrate (1 molecule in assymetric unit) ;
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	22.54 Å
rg_electron	21.56 Å
i0	55001200.00
molecular_weight	57126.0 kDa
excluded_volume	70949 Å³
envelope_volume	79877 Å³
shell_volume	29334 Å³
envelope_diameter	75.7 Å
shell_rg	29.90 Å
envelope_rg	21.95 Å
shape_rg	21.58 Å
total_rg	22.43 Å
total_atoms	4003
n_residues	507
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	71.6 Å
rg_real	22.39 Å
rg_real_error	0.32 Å
i0_real	5.5000e+07
i0_real_error	5.4120e+05
rg_reciprocal	22.43 Å
i0_reciprocal	55000000.0000
total_estimate	0.6857
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	28.2 Å
skewness	0.154
kurtosis	-0.383
angular_range	— – 0.3500 Å⁻¹
current_alpha	0.0000
highest_alpha	18030000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.850; Stabil: 1.000; Sysdev: 0.130; Positv: 1.000; Valcen: 0.980; Smooth: 0.989

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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	59837.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4257

MGSSHHHHHHSSGLVPRGSHMASMKNYTDYFFDEPAFDLHDGGYVPLEVSDAPEKPLNVPPLLKPDKETATDVYYTVTAEAGETQLLPGAKTKTWGYNTSLLGQTIVYRRGQHTHVTLKNTLPELTTFHWHGANVSGPYVDGGCHAPVYPGESKHIDFTLEQPATTLWLHAHPCPSTAEQVWHGLAAMVIVKDDHEASLPLPRNYGVDDIPVILQDRRFHENNQWDYRADYDPDGVAGPTAMINGTINPYFDVTTQKVRLRFLNGANRREWRLHFADDLPFTQIGGDGSLLPEPVKFTHLMLTCAERAEVIVDFGQYHEGDEVTLYTDDVPLLKFRIHAFKPDQTTLPDKLFDVKAPVVDPALPVRHVVMQGMDEGVAIDGKKFAMQRIDATQPIGKAQYWDVTNSNDAPGMVHPFHVHGTQFLVLSRNGHAPYPNEHGFKDTIGVNPGETVRLLVRFDLPGVYMYHCHIIEHLDGGMMAQIETFDPAKPKQEYKLMDMDTLMMALAKERGVKPSEIWMGGMQSYEKMGMKM

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	4

Entity 3 non-polymer

description	SILVER ION
formula_weight	107.9 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	246

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6. Citations (2)

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length_a	126.809 Å
length_b	126.809 Å
length_c	72.981 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 32 2 1
int_tables_number	154
crystal_system	—

resolution	2.100 Å
resolution_low	60.860 Å
r_factor	0.1788
r_work	0.1771
r_free	0.2113

fit	/app/data/saxs_computation/rc/9rc5/9rc5.fit
pddf	/app/data/pr_computation/rc/9rc5/9rc5.pr.out
profile	/app/data/saxs_computation/rc/9rc5/9rc5.dat

;Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 mutant E451L co-crystallized with Silver Nitrate (1 molecule in assymetric unit) ;

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