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9qmn

Pseudomonas putida 4-hydroxyphenylpyruvate dioxygenase in complex with Manganese

Method: X-RAY DIFFRACTION D_max: 97.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qmn
deposition_date	2025-03-23
last_revision	2026-04-08
title	Pseudomonas putida 4-hydroxyphenylpyruvate dioxygenase in complex with Manganese
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	29.89 Å
rg_electron	28.91 Å
i0	89041900.00
molecular_weight	75471.0 kDa
excluded_volume	94753 Å³
envelope_volume	117430 Å³
shell_volume	34087 Å³
envelope_diameter	101.2 Å
shell_rg	36.04 Å
envelope_rg	28.68 Å
shape_rg	28.89 Å
total_rg	29.64 Å
total_atoms	5320
n_residues	667
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	97.1 Å
rg_real	29.90 Å
rg_real_error	0.76 Å
i0_real	8.9040e+07
i0_real_error	1.3480e+06
rg_reciprocal	29.89 Å
i0_reciprocal	89040000.0000
total_estimate	0.8907
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.2 Å
skewness	0.349
kurtosis	-0.407
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	13220000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.893

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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	5752

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	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	nat
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	391

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6. Citations (1)

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length_a	149.556 Å
length_b	170.579 Å
length_c	76.024 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	2.050 Å
resolution_low	56.750 Å
r_factor	0.2573
r_work	0.2562
r_free	0.2764

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

Pseudomonas putida 4-hydroxyphenylpyruvate dioxygenase in complex with Manganese

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