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13pk

TERNARY COMPLEX OF PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI

Method: X-RAY DIFFRACTION D_max: 139.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	13pk
deposition_date	1996-11-23
title	TERNARY COMPLEX OF PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI
keywords	KINASE, PHOSPHOGLYCERATE, TERNARY COMPLEX, GLYCOLYSIS, TRANSFERASE; KINASE
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	41.75 Å
rg_electron	41.63 Å
i0	484053000.00
molecular_weight	181340.0 kDa
excluded_volume	227720 Å³
envelope_volume	283910 Å³
shell_volume	57592 Å³
envelope_diameter	145.7 Å
shell_rg	46.39 Å
envelope_rg	41.10 Å
shape_rg	41.64 Å
total_rg	41.83 Å
total_atoms	12672
n_residues	1660
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	139.9 Å
rg_real	41.88 Å
rg_real_error	1.24 Å
i0_real	4.8410e+08
i0_real_error	8.5190e+06
rg_reciprocal	41.75 Å
i0_reciprocal	484000000.0000
total_estimate	0.8720
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	44.2 Å
skewness	0.401
kurtosis	-0.458
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	50620000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.860; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.772

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	3-PHOSPHOGLYCERATE KINASE
formula_weight	44700.0 kDa
ec_number	2.7.2.3
mutation	TRUNCATION OF T. BRUCEI SPECIFIC C-TERMINAL SEQUENCE
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	13271

EKKSINECDLKGKKVLIRVDFNVPVKNGKITNDYRIRSALPTLKKVLTEGGSCVLMSHLGRPKGIPMAQAGKIRSTGGVPGFQQKATLKPVAKRLSELLLRPVTFAPDCLNAADVVSKMSPGDVVLLENVRFYKEEGSKKAKDREAMAKILASYGDVYISDAFGTAHRDSATMTGIPKILGNGAAGYLMEKEISYFAKVLGNPPRPLVAIVGGAKVSDKIQLLDNMLQRIDYLLIGGAMAYTFLKAQGYSIGKSKCEESKLEFARSLLKKAEDRKVQVILPIDHVCHTEFKAVDSPLITEDQNIPEGHMALDIGPKTIEKYVQTIGKCKSAIWNGPMGVFEMVPYSKGTFAIAKAMGRGTHEHGLMSIIGGGDSASAAELSGEAKRMSHVSTGGGASLELLEGKTLPGVTVLDDK

Source

organism	Trypanosoma brucei
ncbi_taxonomy_id	5691
host_organism	Escherichia coli BL21

Entity 2 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	6

Entity 4 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

description	3-PHOSPHOGLYCERIC ACID
formula_weight	186.1 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	599

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6. Citations (1)

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length_a	113.213 Å
length_b	115.959 Å
length_c	171.327 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.500 Å
resolution_low	8.000 Å
r_factor	0.2206
r_work	0.2206
r_free	0.2910

fit	/app/data/saxs_computation/3p/13pk/13pk.fit
pddf	/app/data/pr_computation/3p/13pk/13pk.pr.out
profile	/app/data/saxs_computation/3p/13pk/13pk.dat