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9t62

Crystal structure of ortho-aminophenol oxidase SmNspF from Streptomyces murayamaensis

Method: X-RAY DIFFRACTION D_max: 98.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t62
deposition_date	2025-11-06
title	Crystal structure of ortho-aminophenol oxidase SmNspF from Streptomyces murayamaensis
keywords	type-III copper enzyme, polyphenol oxidase, nitroso-forming activity, C-nitrosation, OXIDOREDUCTASE; 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	30.49 Å
rg_electron	30.12 Å
i0	80936800.00
molecular_weight	70517.0 kDa
excluded_volume	87620 Å³
envelope_volume	105090 Å³
shell_volume	29911 Å³
envelope_diameter	101.7 Å
shell_rg	36.19 Å
envelope_rg	29.87 Å
shape_rg	30.12 Å
total_rg	30.62 Å
total_atoms	4983
n_residues	599
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	98.4 Å
rg_real	30.66 Å
rg_real_error	0.65 Å
i0_real	8.0940e+07
i0_real_error	1.1700e+06
rg_reciprocal	30.59 Å
i0_reciprocal	80930000.0000
total_estimate	0.8479
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	26.5 Å
skewness	0.390
kurtosis	-0.695
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	25630000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.775; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.823; Smooth: 0.871

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	O-aminophenol oxidase
formula_weight	35887.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5010

GPMTHVRRNHLDLSRSERRRFIKAVLEIKRRGIYDRFVKLHVDVNSQDYLDKDTGKRVGHINPGFFPWHRQYLMEFEKELRRVDPTVTLPYWDWTMDQSKDSPLWQDDFMGGDGRPDDGMVMTGPFAYPNGWELKVNVQPEGPESPALNGHYTVDDRKFLIRRIGQKLPSLPSPEQLQQTMDLPVYDCPPWNYTSGSTPPYNSFRNHLEGYTNFAWEPPAGKLHGAGHQWVGGHMMYISSPNDPVFFLHHCFIDKIWGDWQALHPDVPHYLPQEPTPEVADPSTPLYPWHTKTVAEVIDHRRFYTYA

Source

organism	Streptomyces murayamaensis
ncbi_taxonomy_id	224537
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	COPPER (II) ION
formula_weight	63.5 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	23

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6. Citations (1)

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length_a	86.189 Å
length_b	86.189 Å
length_c	88.245 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 3
int_tables_number	143
crystal_system	—

resolution	2.400 Å
resolution_low	74.640 Å
r_factor	—
r_work	0.1827
r_free	0.2376

fit	/app/data/saxs_computation/t6/9t62/9t62.fit
pddf	/app/data/pr_computation/t6/9t62/9t62.pr.out
profile	/app/data/saxs_computation/t6/9t62/9t62.dat

Crystal structure of ortho-aminophenol oxidase SmNspF from Streptomyces murayamaensis

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