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9qmg

Pseudomonas putida 4-hydroxyphenylpyruvate dioxygenase in complex with Tefuryltrione (Mn)

Method: X-RAY DIFFRACTION D_max: 112.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qmg
deposition_date	2025-03-23
last_revision	2026-04-08
title	Pseudomonas putida 4-hydroxyphenylpyruvate dioxygenase in complex with Tefuryltrione (Mn)
keywords	;Dioxygenase, Phenylalanine catabolism, Tyrosine catabolism, Iron, Metal-binding, 4-hydroxyphenylpyruvate, homogentisic acid, 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	36.86 Å
rg_electron	36.22 Å
i0	668746000.00
molecular_weight	141730.0 kDa
excluded_volume	137770 Å³
envelope_volume	245490 Å³
shell_volume	55631 Å³
envelope_diameter	115.2 Å
shell_rg	43.17 Å
envelope_rg	35.84 Å
shape_rg	36.20 Å
total_rg	36.56 Å
total_atoms	10728
n_residues	1332
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	112.5 Å
rg_real	36.64 Å
rg_real_error	0.68 Å
i0_real	6.6870e+08
i0_real_error	1.0070e+07
rg_reciprocal	36.78 Å
i0_reciprocal	668800000.0000
total_estimate	0.8369
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	49.7 Å
skewness	0.065
kurtosis	-0.678
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	74760000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	4-hydroxyphenylpyruvate dioxygenase
formula_weight	40473.9 kDa
ec_number	1.13.11.27
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	11039

GGSSADIFDNPMGLMGFEFIELASPTPGVLEPVFQMLGFTKVATHRSKDVHLYRQGDINLILNNEPKSIASYFAAEHGPSVCGMAFRVRNAHEAYARALELGAQPVEIETGPMELRLPAIKGIGGAPLYLIDRFEEGSSIYDIDFKFIEGVDRNPVGAGLKIIDHLTHNVYRGRMSYWAGFYEKLFNFREIRYFDIKGEYTGLTSRAMTAPDGMIRIPLNEESSKGSGQIEEFLMQFNGEGIQHVAFLTDDLLKTWDALKGFGMRFMTAPPQTYYEMLEERLPGHGEPVDQLKARGILLDGASQPDDKRLLLQIFSETLLGPVFFEFIQRKGDDGFGEGNFKALFESIERDQVRRGVLSTD

Source

organism	Pseudomonas putida
ncbi_taxonomy_id	303
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	Tefuryltrione
formula_weight	442.9 kDa
src_method	nat
entity_count	4

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	267

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6. Citations (1)

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length_a	151.190 Å
length_b	169.242 Å
length_c	79.577 Å
angle_alpha	90.00 °
angle_beta	91.88 °
angle_gamma	90.00 °
z_pdb	16

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.700 Å
resolution_low	45.460 Å
r_factor	0.2481
r_work	0.2462
r_free	0.2862

fit	/app/data/saxs_computation/qm/9qmg/9qmg.fit
pddf	/app/data/pr_computation/qm/9qmg/9qmg.pr.out
profile	/app/data/saxs_computation/qm/9qmg/9qmg.dat

Pseudomonas putida 4-hydroxyphenylpyruvate dioxygenase in complex with Tefuryltrione (Mn)

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