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9u42

Crystal Structure of Homogentisate 1,2-Dioxygenase from Acinetobacter in Complex with Zn ion

Method: X-RAY DIFFRACTION D_max: 68.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u42
deposition_date	2025-03-19
title	Crystal Structure of Homogentisate 1,2-Dioxygenase from Acinetobacter in Complex with Zn ion
keywords	Dioxygenase, Aromatic compound metabolism, 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	20.45 Å
rg_electron	19.49 Å
i0	7287040.00
molecular_weight	19791.0 kDa
excluded_volume	24781 Å³
envelope_volume	33468 Å³
shell_volume	15381 Å³
envelope_diameter	68.3 Å
shell_rg	24.26 Å
envelope_rg	19.49 Å
shape_rg	19.45 Å
total_rg	20.40 Å
total_atoms	1403
n_residues	169
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	68.4 Å
rg_real	20.42 Å
rg_real_error	0.46 Å
i0_real	7.2870e+06
i0_real_error	9.4990e+04
rg_reciprocal	20.42 Å
i0_reciprocal	7287000.0000
total_estimate	0.8936
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.4 Å
skewness	0.215
kurtosis	-0.513
angular_range	— – 0.3900 Å⁻¹
current_alpha	0.0000
highest_alpha	543300.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.998

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Glyoxalase
formula_weight	21229.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1568

MTFAIKKIHHVAYRCKDAKETVEWYKKMLNMDFILAFAEDHVPSTKAFDPYMHLFLDAGQGNVLAFFELPTQPEMGRDENTPQWVQHIAFEVEDVNALMAAKQHLEENGVKVLGVTNHGIFHSIYFFDPNGHRLELTYNDVRAEEKIAKITEEMKAEMLEEWSKTKRAPHHTHFLHEEELGT

Source

organism	Acinetobacter
ncbi_taxonomy_id	469
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	122.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	165

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6. Citations (1)

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length_a	53.058 Å
length_b	121.250 Å
length_c	54.363 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	1.550 Å
resolution_low	24.800 Å
r_factor	0.1695
r_work	0.1687
r_free	0.1909

fit	/app/data/saxs_computation/u4/9u42/9u42.fit
pddf	/app/data/pr_computation/u4/9u42/9u42.pr.out
profile	/app/data/saxs_computation/u4/9u42/9u42.dat

Crystal Structure of Homogentisate 1,2-Dioxygenase from Acinetobacter in Complex with Zn ion

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