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9tme

Structure of Plasmodium falciparum Transketolase in complex with Oxythiamine

Method: X-RAY DIFFRACTION D_max: 168.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9tme
deposition_date	2025-12-12
last_revision	2026-01-28
title	Structure of Plasmodium falciparum Transketolase in complex with Oxythiamine
keywords	Malaria, inhibitor, transketolase, 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	49.13 Å
rg_electron	49.24 Å
i0	2550330000.00
molecular_weight	280490.0 kDa
excluded_volume	271480 Å³
envelope_volume	472280 Å³
shell_volume	78413 Å³
envelope_diameter	172.4 Å
shell_rg	53.84 Å
envelope_rg	48.97 Å
shape_rg	49.26 Å
total_rg	49.32 Å
total_atoms	21247
n_residues	2658
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	168.4 Å
rg_real	49.34 Å
rg_real_error	1.79 Å
i0_real	2.5500e+09
i0_real_error	5.0640e+07
rg_reciprocal	49.14 Å
i0_reciprocal	2550000000.0000
total_estimate	0.7951
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	47.4 Å
skewness	0.366
kurtosis	-0.592
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	129300000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.794; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.951; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	transketolase
formula_weight	75910.0 kDa
ec_number	2.2.1.1
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	23239

MNIMDNEIDTKCINEIRMLSAELPLEAKSGHQGAPIGCAPIAHILWSYVMNYYNEDTKWINRDRFILSNGHASALLYTMLYLTEQGLSMEDLKSFRQFGSLTPGHPENHITKGVEVTTGPLGQGASNAVGMAIAAHNLADKYNTEEHKIFDNYVYAICGDGCMQEGVFCEAASLAGHLGLGRLILLYDDNKITIDGNTDLSFTENIEKKFEALNWEVRRVEDGNKDYKKILHEIEQGKKNLQQPTLIIVRTACGFGTKVEGTCKSHGLALNDEDLKNAKSFFGLDPQKKFHISDEVKEFYKNVIQKKKENYIKWKNMFDDFSLKYPQVSQEIIRRFQNDLPNNWKDALPKYTPKDAPGATRNLSGIVLNSINKIFPELIGGSADLSESNCTSLKEENDIKKNSYGNKYIRFGVREHGMVAITNGLYAYGGFKPYCGTFLNFYTYAFGALRLAALSNHHILCIATHDSVELGEDGPTHQPIEVLSLLRSTPNLNIIRPADGNEVSGAYLSHFSNPHTPTVIALCRNKVPHLNNTQPEQVLKGAYILEDFDTSNNPKVILTGSGSELHLCFEAKEILKNQHQLNVRIVSFPSWTLFKKQPEDYQYSVMMHNHPNLPRFYIEPASTHGFDTYFNVYIGINQFGYSAPKNKIWEHLGFTPENIVQKVLAFMKNKLK

Source

organism	Plasmodium falciparum 3D7
ncbi_taxonomy_id	36329
host_organism	Escherichia coli

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	6

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	Oxythiamine
formula_weight	266.3 kDa
src_method	syn
entity_count	4

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1981

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6. Citations (1)

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length_a	114.388 Å
length_b	142.810 Å
length_c	176.185 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.813 Å
resolution_low	110.942 Å
r_factor	—
r_work	0.1809
r_free	0.2170

fit	/app/data/saxs_computation/tm/9tme/9tme.fit
pddf	/app/data/pr_computation/tm/9tme/9tme.pr.out
profile	/app/data/saxs_computation/tm/9tme/9tme.dat