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9zk4

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

Method: X-RAY DIFFRACTION D_max: 72.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zk4
deposition_date	2025-12-05
last_revision	2025-12-17
title	Crystal structure of a malonate 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	21.82 Å
rg_electron	20.91 Å
i0	15510800.00
molecular_weight	31126.0 kDa
excluded_volume	39606 Å³
envelope_volume	47589 Å³
shell_volume	19391 Å³
envelope_diameter	76.1 Å
shell_rg	26.91 Å
envelope_rg	21.37 Å
shape_rg	20.88 Å
total_rg	21.90 Å
total_atoms	2194
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	72.3 Å
rg_real	21.78 Å
rg_real_error	0.56 Å
i0_real	1.5510e+07
i0_real_error	2.1570e+05
rg_reciprocal	21.78 Å
i0_reciprocal	15510000.0000
total_estimate	0.8088
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	23.7 Å
skewness	0.257
kurtosis	-0.439
angular_range	— – 0.3650 Å⁻¹
current_alpha	0.0000
highest_alpha	3852000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.853; Stabil: 0.995; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.000

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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	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	2521

MAHHHHHHMYQLHVRVVEAKELPKMDTFGKCDAFAILQLNSSRNIHRTKVIEKTYTPVWNEEFHIPLEDVTIDTLTVFLKDEDKGSSDDPISLIKIPINQFPLGEVVDKWYSLIPVKGVKKGGQIRLTIHIAPLGATPFQKTD

Source

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

Entity 2 non-polymer

description	MALONATE ION
formula_weight	102.0 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	249

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6. Citations (1)

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length_a	25.206 Å
length_b	82.360 Å
length_c	56.780 Å
angle_alpha	90.00 °
angle_beta	96.61 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.300 Å
resolution_low	46.540 Å
r_factor	0.1435
r_work	0.1420
r_free	0.1708

fit	/app/data/saxs_computation/zk/9zk4/9zk4.fit
pddf	/app/data/pr_computation/zk/9zk4/9zk4.pr.out
profile	/app/data/saxs_computation/zk/9zk4/9zk4.dat