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9zk0

Crystal structure of a calcium bound C2 domain containing protein from Trichomonas vaginalis

Method: X-RAY DIFFRACTION D_max: 76.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zk0
deposition_date	2025-12-05
last_revision	2025-12-17
title	Crystal structure of a calcium bound C2 domain containing protein from Trichomonas vaginalis
keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, C2 domain, LIPID BINDING PROTEIN; LIPID BINDING PROTEIN
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	21.67 Å
rg_electron	20.53 Å
i0	15623100.00
molecular_weight	31177.0 kDa
excluded_volume	39696 Å³
envelope_volume	47679 Å³
shell_volume	19626 Å³
envelope_diameter	77.7 Å
shell_rg	26.53 Å
envelope_rg	20.94 Å
shape_rg	20.49 Å
total_rg	21.55 Å
total_atoms	2196
n_residues	272
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	76.0 Å
rg_real	21.62 Å
rg_real_error	0.57 Å
i0_real	1.5620e+07
i0_real_error	2.1410e+05
rg_reciprocal	21.63 Å
i0_reciprocal	15620000.0000
total_estimate	0.8670
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.8 Å
skewness	0.261
kurtosis	-0.404
angular_range	— – 0.3650 Å⁻¹
current_alpha	0.0000
highest_alpha	4161000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.785; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.923; Smooth: 0.989

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	C2 domain containing protein
formula_weight	16382.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	2493

MAHHHHHHMYQLHVRVVEAKELPKMDTFGKCDAFAILQLNSSRNIHRTKVIEKTYTPVWNEEFHIPLEDVTIDTLTVFLKDEDKGSSDDPISLIKIPINQFPLGEVVDKWYSLIPVKGVKKGGQIRLTIHIAPLGATPFQKTD

Source

organism	Trichomonas vaginalis G3
ncbi_taxonomy_id	412133
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	PENTAETHYLENE GLYCOL
formula_weight	238.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	TRIETHYLENE GLYCOL
formula_weight	150.2 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	274

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6. Citations (1)

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length_a	25.329 Å
length_b	50.197 Å
length_c	56.300 Å
angle_alpha	74.23 °
angle_beta	82.17 °
angle_gamma	79.99 °
z_pdb	2

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	1.400 Å
resolution_low	47.810 Å
r_factor	0.1419
r_work	0.1404
r_free	0.1699

fit	/app/data/saxs_computation/zk/9zk0/9zk0.fit
pddf	/app/data/pr_computation/zk/9zk0/9zk0.pr.out
profile	/app/data/saxs_computation/zk/9zk0/9zk0.dat