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9zk5

Crystal structure of a calcium bound C2 domain containing protein from Trichomonas vaginalis (P61 form)

Method: X-RAY DIFFRACTION D_max: 62.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zk5
deposition_date	2025-12-05
last_revision	2025-12-17
title	Crystal structure of a calcium bound C2 domain containing protein from Trichomonas vaginalis (P61 form)
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	17.23 Å
rg_electron	16.03 Å
i0	4707130.00
molecular_weight	16324.0 kDa
excluded_volume	20770 Å³
envelope_volume	23646 Å³
shell_volume	13012 Å³
envelope_diameter	63.8 Å
shell_rg	21.21 Å
envelope_rg	16.57 Å
shape_rg	15.97 Å
total_rg	17.22 Å
total_atoms	1143
n_residues	139
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	62.0 Å
rg_real	17.27 Å
rg_real_error	0.65 Å
i0_real	4.7070e+06
i0_real_error	6.6240e+04
rg_reciprocal	17.26 Å
i0_reciprocal	4707000.0000
total_estimate	0.8327
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	19.6 Å
skewness	0.427
kurtosis	-0.164
angular_range	— – 0.4600 Å⁻¹
current_alpha	0.0000
highest_alpha	951100.0000
n_real_points	77
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.666; Stabil: 0.991; Sysdev: 1.000; Positv: 1.000; Valcen: 0.868; Smooth: 0.984

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	C2 domain containing protein
formula_weight	16382.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1330

MAHHHHHHMYQLHVRVVEAKELPKMDTFGKCDAFAILQLNSSRNIHRTKVIEKTYTPVWNEEFHIPLEDVTIDTLTVFLKDEDKGSSDDPISLIKIPINQFPLGEVVDKWYSLIPVKGVKKGGQIRLTIHIAPLGATPFQKTD

Source

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

Entity 2 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	187

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6. Citations (1)

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length_a	72.280 Å
length_b	72.280 Å
length_c	76.170 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 61
int_tables_number	169
crystal_system	—

resolution	1.540 Å
resolution_low	36.140 Å
r_factor	0.1741
r_work	0.1731
r_free	0.1955

fit	/app/data/saxs_computation/zk/9zk5/9zk5.fit
pddf	/app/data/pr_computation/zk/9zk5/9zk5.pr.out
profile	/app/data/saxs_computation/zk/9zk5/9zk5.dat