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9zk1

Crystal structure of a calcium bound C2 domain containing protein from Trichomonas vaginalis (P21 form)

Method: X-RAY DIFFRACTION D_max: 90.5 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zk1
deposition_date	2025-12-05
last_revision	2025-12-17
title	Crystal structure of a calcium bound C2 domain containing protein from Trichomonas vaginalis (P21 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	28.74 Å
rg_electron	27.87 Å
i0	53203600.00
molecular_weight	60259.0 kDa
excluded_volume	76966 Å³
envelope_volume	97021 Å³
shell_volume	29564 Å³
envelope_diameter	95.7 Å
shell_rg	34.59 Å
envelope_rg	27.68 Å
shape_rg	27.84 Å
total_rg	28.73 Å
total_atoms	4236
n_residues	528
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	90.5 Å
rg_real	28.71 Å
rg_real_error	0.56 Å
i0_real	5.3200e+07
i0_real_error	7.4480e+05
rg_reciprocal	28.73 Å
i0_reciprocal	53200000.0000
total_estimate	0.9117
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	34.5 Å
skewness	0.252
kurtosis	-0.528
angular_range	— – 0.2750 Å⁻¹
current_alpha	0.0000
highest_alpha	6821000.0000
n_real_points	56
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.962; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.977

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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	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	4755

MAHHHHHHMYQLHVRVVEAKELPKMDTFGKCDAFAILQLNSSRNIHRTKVIEKTYTPVWNEEFHIPLEDVTIDTLTVFLKDEDKGSSDDPISLIKIPINQFPLGEVVDKWYSLIPVKGVKKGGQIRLTIHIAPLGATPFQKTD

Source

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

Entity 2 non-polymer

description	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	10

Entity 4 non-polymer

description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
formula_weight	195.2 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	PENTAETHYLENE GLYCOL
formula_weight	238.3 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	495

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6. Citations (1)

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length_a	35.953 Å
length_b	88.059 Å
length_c	97.198 Å
angle_alpha	90.00 °
angle_beta	90.85 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.510 Å
resolution_low	44.030 Å
r_factor	0.1888
r_work	0.1875
r_free	0.2139

fit	/app/data/saxs_computation/zk/9zk1/9zk1.fit
pddf	/app/data/pr_computation/zk/9zk1/9zk1.pr.out
profile	/app/data/saxs_computation/zk/9zk1/9zk1.dat