SAXSdb — 9v5y

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1. Structure Basics

entry_id	9v5y
deposition_date	2025-05-26
title	PfDXR - Mn2+ - SHOK314 ternary complex
keywords	Inhibitor, Malaria, ISOMERASE; ISOMERASE
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	31.18 Å
rg_electron	30.72 Å
i0	262494000.00
molecular_weight	88056.0 kDa
excluded_volume	85775 Å³
envelope_volume	143610 Å³
shell_volume	39172 Å³
envelope_diameter	107.7 Å
shell_rg	37.87 Å
envelope_rg	31.19 Å
shape_rg	30.73 Å
total_rg	31.14 Å
total_atoms	6651
n_residues	822
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	100.6 Å
rg_real	31.25 Å
rg_real_error	0.82 Å
i0_real	2.6250e+08
i0_real_error	4.3080e+06
rg_reciprocal	31.22 Å
i0_reciprocal	262500000.0000
total_estimate	0.8860
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.5 Å
skewness	0.394
kurtosis	-0.443
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	47430000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.883

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic
formula_weight	55829.6 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7212

MKKYIYIYFFFITITINDLVINNTSKCVSIERRKNNAYINYGIGYNGPDNKITKSRRCKRIKLCKKDLIDIGAIKKPINVAIFGSTGSIGTNALNIIRECNKIENVFNVKALYVNKSVNELYEQAREFLPEYLCIHDKSVYEELKELVKNIKDYKPIILCGDEGMKEICSSNSIDKIVIGIDSFQGLYSTMYAIMNNKIVALANKESIVSAGFFLKKLLNIHKNAKIIPVDSEHSAIFQCLDNNKVLKTKCLQDNFSKINNINKIFLCSSGGPFQNLTMDELKNVTSENALKHPKWKMGKKITIDSATMMNKGLEVIETHFLFDVDYNDIEVIVHKECIIHSCVEFIDKSVISQMYYPDMQIPILYSLTWPDRIKTNLKPLDLAQVSTLTFHKPSLEHFPCIKLAYQAGIKGNFYPTVLNASNEIANNLFLNNKIKYFDISSIISQVLESFNSQKVSENSEDLMKQILQIHSWAKDKATDIYNKHNSS

Source

organism	Plasmodium falciparum HB3
ncbi_taxonomy_id	137071
host_organism	Escherichia coli

Entity 2 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	[(1~{S})-4-[4-[1,3-bis(oxidanylidene)isoindol-2-yl]butyl-oxidanyl-amino]-4-oxidanylidene-1-phenyl-butyl]phosphonic acid
formula_weight	460.4 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	3

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	561

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6. Citations (1)

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length_a	51.763 Å
length_b	77.554 Å
length_c	111.486 Å
angle_alpha	90.00 °
angle_beta	92.85 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.570 Å
resolution_low	63.640 Å
r_factor	0.1687
r_work	0.1673
r_free	0.1950

fit	/app/data/saxs_computation/v5/9v5y/9v5y.fit
pddf	/app/data/pr_computation/v5/9v5y/9v5y.pr.out
profile	/app/data/saxs_computation/v5/9v5y/9v5y.dat

PfDXR - Mn2+ - SHOK314 ternary complex

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