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1ex8

CRYSTAL STRUCTURE OF 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE COMPLEXED WITH HP4A, THE TWO-SUBSTRATE-MIMICKING INHIBITOR

Method: X-RAY DIFFRACTION D_max: 46.2 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1ex8
deposition_date	2000-05-01
title	CRYSTAL STRUCTURE OF 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE COMPLEXED WITH HP4A, THE TWO-SUBSTRATE-MIMICKING INHIBITOR
keywords	;PYROPHOSPHOKINASE, PYROPHOSPHORYL TRANSFER, FOLATE, HPPK, PTERIN, ATP, BISUBSTRATE-MIMICKING INHIBITOR, ANTIMICROBIAL AGENT, DRUG DESIGN, SUBSTRATE SPECIFICITY, ACTIVE-SITE ARCHITECTURE, TRANSFERASE ;; TRANSFERASE
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	15.93 Å
rg_electron	14.76 Å
i0	6989170.00
molecular_weight	18767.0 kDa
excluded_volume	23285 Å³
envelope_volume	25547 Å³
shell_volume	14407 Å³
envelope_diameter	48.8 Å
shell_rg	20.87 Å
envelope_rg	14.96 Å
shape_rg	14.77 Å
total_rg	15.82 Å
total_atoms	1317
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	46.2 Å
rg_real	15.78 Å
rg_real_error	0.05 Å
i0_real	6.7450e+06
i0_real_error	4.8650e+04
rg_reciprocal	15.81 Å
i0_reciprocal	6989000.0000
total_estimate	0.7212
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	20.5 Å
skewness	0.072
kurtosis	-0.472
angular_range	— – 0.5000 Å⁻¹
current_alpha	12.5100
highest_alpha	1234000.0000
n_real_points	80
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.965; Stabil: 0.918; Sysdev: 0.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.767

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	6-HYDROXYMETHYL-7,8-DIHYDROPTERIN 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	1484

TVAYIAIGSNLASPLEQVNAALKALGDIPESHILTVSSFYRTPPLGPQDQPDYLNAAVALETSLAPEELLNHTQRIELQQGRVRKAERWGPRTLDLDIMLFGNEVINTERLTVPHYDMKNRGFMLWPLFEIAPELVFPDGEMLRQILHTRAFDKLNKW

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	6-(ADENOSINE TETRAPHOSPHATE-METHYL)-7,8-DIHYDROPTERIN
formula_weight	764.3 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	167

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6. Citations (2)

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length_a	38.053 Å
length_b	61.857 Å
length_c	67.106 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.850 Å
resolution_low	40.000 Å
r_factor	0.1854
r_work	0.2029
r_free	0.2420

fit	/app/data/saxs_computation/ex/1ex8/1ex8.fit
pddf	/app/data/pr_computation/ex/1ex8/1ex8.pr.out
profile	/app/data/saxs_computation/ex/1ex8/1ex8.dat