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9rcm

Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 mutant E451L co-crystallized with Copper Chloride

Method: X-RAY DIFFRACTION D_max: 73.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rcm
deposition_date	2025-05-29
title	Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 mutant E451L 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	22.68 Å
rg_electron	21.65 Å
i0	54882800.00
molecular_weight	57238.0 kDa
excluded_volume	71232 Å³
envelope_volume	81116 Å³
shell_volume	29619 Å³
envelope_diameter	75.8 Å
shell_rg	30.03 Å
envelope_rg	22.07 Å
shape_rg	21.66 Å
total_rg	22.55 Å
total_atoms	4023
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	73.2 Å
rg_real	22.53 Å
rg_real_error	0.34 Å
i0_real	5.4880e+07
i0_real_error	6.1250e+05
rg_reciprocal	22.56 Å
i0_reciprocal	54880000.0000
total_estimate	0.8815
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.7 Å
skewness	0.154
kurtosis	-0.379
angular_range	— – 0.3500 Å⁻¹
current_alpha	0.0000
highest_alpha	19610000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.824; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.999

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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	4191

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	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	168

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6. Citations (2)

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length_a	126.524 Å
length_b	126.524 Å
length_c	74.027 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	2.000 Å
resolution_low	48.140 Å
r_factor	0.2107
r_work	0.2093
r_free	0.2377

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

Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 mutant E451L 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