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9qml

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

Method: X-RAY DIFFRACTION D_max: 95.9 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qml
deposition_date	2025-03-23
last_revision	2026-04-08
title	Pseudomonas putida 4-hydroxyphenylpyruvate dioxygenase in complex with Isoxaflutole (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	29.50 Å
rg_electron	28.78 Å
i0	175381000.00
molecular_weight	71089.0 kDa
excluded_volume	69069 Å³
envelope_volume	118180 Å³
shell_volume	34368 Å³
envelope_diameter	99.8 Å
shell_rg	36.01 Å
envelope_rg	28.61 Å
shape_rg	28.76 Å
total_rg	29.32 Å
total_atoms	5382
n_residues	670
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	95.9 Å
rg_real	29.51 Å
rg_real_error	0.74 Å
i0_real	1.7540e+08
i0_real_error	2.7060e+06
rg_reciprocal	29.51 Å
i0_reciprocal	175400000.0000
total_estimate	0.6808
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	32.0 Å
skewness	0.355
kurtosis	-0.404
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	17520000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 0.092; Positv: 1.000; Valcen: 0.995; Smooth: 0.878

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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	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5947

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	2

Entity 3 non-polymer

description	Isoxaflutole
formula_weight	359.3 kDa
src_method	nat
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	543

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6. Citations (1)

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length_a	149.692 Å
length_b	171.225 Å
length_c	74.971 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	2.000 Å
resolution_low	56.400 Å
r_factor	0.2226
r_work	0.2215
r_free	0.2450

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

Pseudomonas putida 4-hydroxyphenylpyruvate dioxygenase in complex with Isoxaflutole (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