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9qmv

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

Method: X-RAY DIFFRACTION D_max: 72.7 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qmv
deposition_date	2025-03-24
last_revision	2026-04-08
title	;Arabidopsis thaliana 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	21.89 Å
rg_electron	20.66 Å
i0	29850600.00
molecular_weight	41938.0 kDa
excluded_volume	52441 Å³
envelope_volume	61036 Å³
shell_volume	24231 Å³
envelope_diameter	72.6 Å
shell_rg	27.99 Å
envelope_rg	21.01 Å
shape_rg	20.65 Å
total_rg	21.64 Å
total_atoms	2954
n_residues	377
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	72.7 Å
rg_real	21.78 Å
rg_real_error	0.41 Å
i0_real	2.9850e+07
i0_real_error	3.8200e+05
rg_reciprocal	21.80 Å
i0_reciprocal	29850000.0000
total_estimate	0.7241
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	28.2 Å
skewness	0.240
kurtosis	-0.226
angular_range	— – 0.3650 Å⁻¹
current_alpha	0.0000
highest_alpha	6293000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.791; Stabil: 1.000; Sysdev: 0.348; Positv: 1.000; Valcen: 1.000; Smooth: 0.994

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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	45343.0 kDa
ec_number	1.13.11.27
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3255

GGSVRKNPKSDKFKVKRFHHIEFWCGDATNVARRFSWGLGMRFSAKSDLSTGNMVHASYLLTSGDLRFLFTAPYSPSLSAGEIKPTTTASIPSFDHGSCRSFFSSHGLGVRAVAIEVEDAESAFSISVANGAIPSSPPIVLNEAVTIAEVKLYGDVVLRYVSYKAEDTEKSEFLPGFERVEDASSFPLDYGIRRLDHAVGNVPELGPALTYVAGFTGFHQFAEFTADDVGTAESGLNSAVLASNDEMVLLPINEPVHGTKRKSQIQTYLEHNEGAGLQHLALMSEDIFRTLREMRKRSSIGGFDFMPSPPPTYYQNLKKRVGDVLSDDQIKECEELGILVDRDDQGTLLQIFTKPLGDRPTIFIEIIQRVGCMMKDEEGKAYQSGGCGGFGKGNFSELFKSIEEYEKTLEAK

Source

organism	Arabidopsis thaliana
common_name	thale cress
ncbi_taxonomy_id	3702
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

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

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	280

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6. Citations (1)

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length_a	76.971 Å
length_b	84.311 Å
length_c	62.078 Å
angle_alpha	90.00 °
angle_beta	100.20 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	1.700 Å
resolution_low	35.100 Å
r_factor	0.1693
r_work	0.1680
r_free	0.1949

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

;Arabidopsis thaliana 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