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16pk

PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI BISUBSTRATE ANALOG

Method: X-RAY DIFFRACTION D_max: 73.7 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	16pk
deposition_date	1998-05-18
title	PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI BISUBSTRATE ANALOG
keywords	KINASE, PHOSPHOGLYCERATE, TERNARY COMPLEX, GLYCOLYSIS, TRANSFERASE, BISUBSTRATE, ANALOG; 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	23.76 Å
rg_electron	23.05 Å
i0	34436700.00
molecular_weight	45519.0 kDa
excluded_volume	57246 Å³
envelope_volume	67299 Å³
shell_volume	24502 Å³
envelope_diameter	76.6 Å
shell_rg	29.82 Å
envelope_rg	23.02 Å
shape_rg	23.05 Å
total_rg	23.84 Å
total_atoms	3189
n_residues	415
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	73.7 Å
rg_real	23.74 Å
rg_real_error	0.44 Å
i0_real	3.4440e+07
i0_real_error	4.8650e+05
rg_reciprocal	23.74 Å
i0_reciprocal	34440000.0000
total_estimate	0.9014
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	26.5 Å
skewness	0.317
kurtosis	-0.470
angular_range	— – 0.3350 Å⁻¹
current_alpha	0.0000
highest_alpha	6450000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.891

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

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	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3801

EKKSINECDLKGKKVLIRVDFNVPVKNGKITNDYRIRSALPTLKKVLTEGGSCVLMSHLGRPKGIPMAQAGKIRSTGGVPGFQQKATLKPVAKRLSELLLRPVTFAPDCLNAADVVSKMSPGDVVLLENVRFYKEEGSKKAKDREAMAKILASYGDVYISDAFGTAHRDSATMTGIPKILGNGAAGYLMEKEISYFAKVLGNPPRPLVAIVGGAKVSDKIQLLDNMLQRIDYLLIGGAMAYTFLKAQGYSIGKSKCEESKLEFARSLLKKAEDRKVQVILPIDHVCHTEFKAVDSPLITEDQNIPEGHMALDIGPKTIEKYVQTIGKCKSAIWNGPMGVFEMVPYSKGTFAIAKAMGRGTHEHGLMSIIGGGDSASAAELSGEAKRMSHVSTGGGASLELLEGKTLPGVTVLDDK

Source

organism	Trypanosoma brucei
ncbi_taxonomy_id	5691
host_organism	Escherichia coli BL21

Entity 2 non-polymer

description	1,1,5,5-TETRAFLUOROPHOSPHOPENTYLPHOSPHONIC ACID ADENYLATE ESTER
formula_weight	633.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
formula_weight	238.3 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	580

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6. Citations (1)

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length_a	72.710 Å
length_b	79.760 Å
length_c	81.320 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.600 Å
resolution_low	8.000 Å
r_factor	0.1880
r_work	0.1880
r_free	0.2350

fit	/app/data/saxs_computation/6p/16pk/16pk.fit
pddf	/app/data/pr_computation/6p/16pk/16pk.pr.out
profile	/app/data/saxs_computation/6p/16pk/16pk.dat

PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI BISUBSTRATE ANALOG

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction