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9rck

Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 mutant M455A-M456A soaked with Copper 2 minutes

Method: X-RAY DIFFRACTION D_max: 104.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rck
deposition_date	2025-05-29
title	Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 mutant M455A-M456A soaked with Copper 2 minutes
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	31.33 Å
rg_electron	31.10 Å
i0	180239000.00
molecular_weight	104800.0 kDa
excluded_volume	129520 Å³
envelope_volume	155090 Å³
shell_volume	41436 Å³
envelope_diameter	112.9 Å
shell_rg	38.15 Å
envelope_rg	31.41 Å
shape_rg	31.12 Å
total_rg	31.58 Å
total_atoms	7348
n_residues	932
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	104.1 Å
rg_real	31.42 Å
rg_real_error	0.78 Å
i0_real	1.8020e+08
i0_real_error	2.5680e+06
rg_reciprocal	31.39 Å
i0_reciprocal	180200000.0000
total_estimate	0.8572
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	34.7 Å
skewness	0.450
kurtosis	-0.301
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	58280000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.815; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.955; Smooth: 0.742

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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	59733.3 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	C,A,B,E
atom_count	7594

MGSSHHHHHHSSGLVPRGSHMASMKNYTDYFFDEPAFDLHDGGYVPLEVSDAPEKPLNVPPLLKPDKETATDVYYTVTAEAGETQLLPGAKTKTWGYNTSLLGQTIVYRRGQHTHVTLKNTLPELTTFHWHGANVSGPYVDGGCHAPVYPGESKHIDFTLEQPATTLWLHAHPCPSTAEQVWHGLAAMVIVKDDHEASLPLPRNYGVDDIPVILQDRRFHENNQWDYRADYDPDGVAGPTAMINGTINPYFDVTTQKVRLRFLNGANRREWRLHFADDLPFTQIGGDGSLLPEPVKFTHLMLTCAERAEVIVDFGQYHEGDEVTLYTDDVPLLKFRIHAFKPDQTTLPDKLFDVKAPVVDPALPVRHVVMQGMDEGVAIDGKKFAMQRIDATQPIGKAQYWDVTNSNDAPGMVHPFHVHGTQFLVLSRNGHAPYPNEHGFKDTIGVNPGETVRLLVRFDLPGVYMYHCHIIEHEDGGAAAQIETFDPAKPKQEYKLMDMDTLMMALAKERGVKPSEIWMGGMQSYEKMGMKM

Source

organism	Pediococcus pentosaceus 4618
ncbi_taxonomy_id	1255
host_organism	Escherichia coli K-12

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	COPPER (II) ION
formula_weight	63.5 kDa
src_method	syn
entity_count	21

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	236

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6. Citations (2)

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length_a	123.115 Å
length_b	123.115 Å
length_c	179.736 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	24

space_group	P 32 2 1
int_tables_number	154
crystal_system	—

resolution	2.300 Å
resolution_low	52.290 Å
r_factor	0.1893
r_work	0.1879
r_free	0.2170

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

Laccase (multicopper oxidase) from Pediococcus pentosaceus 4618 mutant M455A-M456A soaked with Copper 2 minutes

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