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9zax

Crystal structure of Phosphoglycerate mutase from Trichomonas vaginalis in complex with 3-phosphoglyceric acid

Method: X-RAY DIFFRACTION D_max: 98.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zax
deposition_date	2025-11-19
last_revision	2025-12-03
title	Crystal structure of Phosphoglycerate mutase from Trichomonas vaginalis in complex with 3-phosphoglyceric acid
keywords	;SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, TRANSFERASE, Phosphoglycerate mutase, ISOMERASE ;; ISOMERASE
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	30.35 Å
rg_electron	29.06 Å
i0	178054000.00
molecular_weight	104590.0 kDa
excluded_volume	130270 Å³
envelope_volume	161940 Å³
shell_volume	44858 Å³
envelope_diameter	105.8 Å
shell_rg	37.52 Å
envelope_rg	29.17 Å
shape_rg	29.01 Å
total_rg	29.96 Å
total_atoms	7319
n_residues	900
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	98.6 Å
rg_real	30.19 Å
rg_real_error	0.57 Å
i0_real	1.7810e+08
i0_real_error	2.3620e+06
rg_reciprocal	30.26 Å
i0_reciprocal	178100000.0000
total_estimate	0.8876
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	39.8 Å
skewness	0.188
kurtosis	-0.339
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	66310000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.995

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Phosphoglycerate mutase
formula_weight	29929.2 kDa
ec_number	5.4.2.11
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	7786

MAHHHHHHMSRKKIEPFSTLVILRHGESLSNLNRTYSGWYDTDLTEKGIEDAYAAGRLLKSHGFHFDVCFSSYLKRSIRTMWIVLDVLDQMHIQTISNWRLNECHFGLLTGMNKEQICTTLTEEELNIWKKDTCLQPPPCAPGQENPSDDPKYKDLDPRVIPNGESIDMMWERAKPYFIDQIVPRLMEGKKVLIVAHGNVMRAMKKYLQKMTSEELMNEKVLSNGSALVFKFDNKFNLLETEIISEEDATIEANDGVL

Source

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

Entity 2 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	3-PHOSPHOGLYCERIC ACID
formula_weight	186.1 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	TETRAETHYLENE GLYCOL
formula_weight	194.2 kDa
src_method	syn
entity_count	10

Entity 5 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	5

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	455

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6. Citations (1)

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length_a	74.639 Å
length_b	93.061 Å
length_c	95.485 Å
angle_alpha	90.00 °
angle_beta	92.86 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.100 Å
resolution_low	48.830 Å
r_factor	0.1796
r_work	0.1779
r_free	0.2126

fit	/app/data/saxs_computation/za/9zax/9zax.fit
pddf	/app/data/pr_computation/za/9zax/9zax.pr.out
profile	/app/data/saxs_computation/za/9zax/9zax.dat