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1dy3

Ternary complex of 7,8-dihydro-6-hydroxymethylpterinpyrophosphokinase from Escherichia coli with ATP and a substrate analogue.

Method: X-RAY DIFFRACTION D_max: 47.3 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dy3
deposition_date	2000-01-21
title	Ternary complex of 7,8-dihydro-6-hydroxymethylpterinpyrophosphokinase from Escherichia coli with ATP and a substrate analogue.
keywords	PYROPHOSPHORYLASE, DE NOVO FOLATE BIOSYNTHESIS; PYROPHOSPHORYLASE
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	15.92 Å
rg_electron	14.76 Å
i0	6762620.00
molecular_weight	18812.0 kDa
excluded_volume	23465 Å³
envelope_volume	25891 Å³
shell_volume	14539 Å³
envelope_diameter	44.9 Å
shell_rg	21.01 Å
envelope_rg	14.99 Å
shape_rg	14.78 Å
total_rg	15.83 Å
total_atoms	1323
n_residues	158
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	47.3 Å
rg_real	15.80 Å
rg_real_error	0.22 Å
i0_real	6.7630e+06
i0_real_error	6.4280e+04
rg_reciprocal	15.81 Å
i0_reciprocal	6763000.0000
total_estimate	0.9071
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	46.1 Å
skewness	0.070
kurtosis	-0.490
angular_range	— – 0.5000 Å⁻¹
current_alpha	0.0000
highest_alpha	1220000.0000
n_real_points	80
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.988

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
formula_weight	17966.5 kDa
ec_number	2.7.6.3
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1464

TVAYIAIGSNLASPLEQVNAALKALGDIPESHILTVSSFYRTPPLGPQDQPDYLNAAVALETSLAPEELLNHTQRIELQQGRVRKAERWGPRTLDLDIMLFGNEVINTERLTVPHYDMKNRGFMLWPLFEIAPELVFPDGEMLRQILHTRAFDKLNKW

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	ESCHERICHIA COLI

Entity 2 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	7,8-DIHYDRO-6-HYDROXYMETHYL-7-METHYL-7-[2-PHENYLETHYL]-PTERIN
formula_weight	313.4 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	141

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6. Citations (1)

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length_a	40.960 Å
length_b	69.010 Å
length_c	115.490 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	2.000 Å
resolution_low	10.000 Å
r_factor	—
r_work	0.1650
r_free	—

fit	/app/data/saxs_computation/dy/1dy3/1dy3.fit
pddf	/app/data/pr_computation/dy/1dy3/1dy3.pr.out
profile	/app/data/saxs_computation/dy/1dy3/1dy3.dat