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9tk5

Room temperature structure of urocanate reductase in complex with urocanate in citrate condition

Method: X-RAY DIFFRACTION D_max: 79.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9tk5
deposition_date	2025-12-08
title	Room temperature structure of urocanate reductase in complex with urocanate in citrate condition
keywords	urocanate reductase, 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	23.33 Å
rg_electron	22.68 Å
i0	42950300.00
molecular_weight	50110.0 kDa
excluded_volume	62438 Å³
envelope_volume	71204 Å³
shell_volume	26172 Å³
envelope_diameter	82.6 Å
shell_rg	30.04 Å
envelope_rg	23.02 Å
shape_rg	22.67 Å
total_rg	23.53 Å
total_atoms	3524
n_residues	454
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	79.9 Å
rg_real	23.35 Å
rg_real_error	0.50 Å
i0_real	4.2950e+07
i0_real_error	5.3840e+05
rg_reciprocal	23.35 Å
i0_reciprocal	42950000.0000
total_estimate	0.8600
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.8 Å
skewness	0.466
kurtosis	-0.079
angular_range	— – 0.3400 Å⁻¹
current_alpha	0.0000
highest_alpha	13040000.0000
n_real_points	66
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.742; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.968

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Urocanate reductase
formula_weight	49984.5 kDa
ec_number	1.3.99.33
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3862

MEYTYDVVIIGSGGAGFSAGLEAIAAGRSAVIIEKMPIIGGNSLISGAEMNVAGSWVQKNMGITDSKELFISDTLKGGDFKGDPEMVKTMVDNAVGAAEWLRDYVKVEFYPDQLFQFGGHSVKRALIPKGHTGAEVISKFSIKADEVGLPIHTNTKAEKLIQDQTGRIVGVEAAHNGKTITYHAKRGVVIATGGFSSNMEMRKKYNPELDERYGSTGHAGGTGDGIVMAEKIHAAAKNMGYIQSYPICSPTSGAIALIADSRFFGAVLINQKGERFVEELERRDVISHAILAQPGRYTYVLWNQDIENVAHTVEMHQGELKEFTKDGLMYKVDTLEEAAKVFNIPEDKLLSTIKDVNHYAATGKDEAFNHRSGLVDLSKGPYWILKATPSVHHTMGGLVVDTRTRVLDEQGKVIPGLFAAGEVTGLTHGTNRLGGNAYTDIIVYGRIAGQEAAKHHHHHH

Source

organism	Shewanella oneidensis MR-1
ncbi_taxonomy_id	211586
host_organism	Escherichia coli

Entity 2 non-polymer

description	FLAVIN-ADENINE DINUCLEOTIDE
formula_weight	785.5 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	(2E)-3-(1H-IMIDAZOL-4-YL)ACRYLIC ACID
formula_weight	138.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	280

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6. Citations (1)

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length_a	126.176 Å
length_b	126.176 Å
length_c	66.729 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 31 2 1
int_tables_number	152
crystal_system	trigonal

resolution	1.800 Å
resolution_low	31.970 Å
r_factor	0.1501
r_work	0.1491
r_free	0.1690

fit	/app/data/saxs_computation/tk/9tk5/9tk5.fit
pddf	/app/data/pr_computation/tk/9tk5/9tk5.pr.out
profile	/app/data/saxs_computation/tk/9tk5/9tk5.dat