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9qmk

;Pseudomonas putida 4-hydroxyphenylpyruvate dioxygenase in complex with 2-(2-nitro-4-trifluoromethylbenzoyl)-1, 3-cyclohexanedione (NTBC) (Mn) ;

Method: X-RAY DIFFRACTION D_max: 96.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qmk
deposition_date	2025-03-23
last_revision	2026-04-08
title	;Pseudomonas putida 4-hydroxyphenylpyruvate dioxygenase in complex with 2-(2-nitro-4-trifluoromethylbenzoyl)-1, 3-cyclohexanedione (NTBC) (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	29.68 Å
rg_electron	28.69 Å
i0	91064200.00
molecular_weight	76092.0 kDa
excluded_volume	95410 Å³
envelope_volume	117360 Å³
shell_volume	34208 Å³
envelope_diameter	100.1 Å
shell_rg	35.92 Å
envelope_rg	28.58 Å
shape_rg	28.67 Å
total_rg	29.43 Å
total_atoms	5364
n_residues	668
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	96.5 Å
rg_real	29.68 Å
rg_real_error	0.70 Å
i0_real	9.1060e+07
i0_real_error	1.3410e+06
rg_reciprocal	29.68 Å
i0_reciprocal	91060000.0000
total_estimate	0.8904
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	32.8 Å
skewness	0.352
kurtosis	-0.391
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	14220000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.895

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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	5891

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	2-{HYDROXY[2-NITRO-4-(TRIFLUOROMETHYL)PHENYL]METHYLENE}CYCLOHEXANE-1,3-DIONE
formula_weight	329.2 kDa
src_method	nat
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	472

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6. Citations (1)

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length_a	148.671 Å
length_b	170.517 Å
length_c	75.305 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	56.440 Å
r_factor	0.2216
r_work	0.2195
r_free	0.2613

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

;Pseudomonas putida 4-hydroxyphenylpyruvate dioxygenase in complex with 2-(2-nitro-4-trifluoromethylbenzoyl)-1, 3-cyclohexanedione (NTBC) (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