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11ko

Structure of Escherichia coli phosphoenolpyruvate carboxykinase with bound ATP, Mg2+, and Mn2+

Method: X-RAY DIFFRACTION D_max: 77.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	11ko
deposition_date	2026-03-02
last_revision	2026-04-29
title	Structure of Escherichia coli phosphoenolpyruvate carboxykinase with bound ATP, Mg2+, and Mn2+
keywords	PEPCK, PCKA, adenyl nucleotide binding, LYASE; LYASE
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	24.02 Å
rg_electron	22.97 Å
i0	58000300.00
molecular_weight	59107.0 kDa
excluded_volume	73784 Å³
envelope_volume	85131 Å³
shell_volume	29838 Å³
envelope_diameter	80.9 Å
shell_rg	30.97 Å
envelope_rg	23.19 Å
shape_rg	22.98 Å
total_rg	23.79 Å
total_atoms	4162
n_residues	530
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	77.4 Å
rg_real	23.90 Å
rg_real_error	0.40 Å
i0_real	5.8000e+07
i0_real_error	7.2100e+05
rg_reciprocal	23.93 Å
i0_reciprocal	58000000.0000
total_estimate	0.8894
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.0 Å
skewness	0.244
kurtosis	-0.343
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	18440000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.863; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.971

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Phosphoenolpyruvate carboxykinase (ATP)
formula_weight	59732.2 kDa
ec_number	4.1.1.49
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4596

GPRVNNGLTPQELEAYGISDVHDIVYNPSYDLLYQEELDPSLTGYERGVLTNLGAVAVDTGIFTGRSPKDKYIVRDDTTRDTFWWADKGKGKNDNKPLSPETWQHLKGLVTRQLSGKRLFVVDAFCGANPDTRLSVRFITEVAWQAHFVKNMFIRPSDEELAGFKPDFIVMNGAKCTNPQWKEQGLNSENFVAFNLTERMQLIGGTWYGGEMKKGMFSMMNYLLPLKGIASMHCSANVGEKGDVAVFFGLSGTGKTTLSTDPKRRLIGDDEHGWDDDGVFNFEGGCYAKTIKLSKEAEPEIYNAIRRDALLENVTVREDGTIDFDDGSKTENTRVSYPIYHIDNIVKPVSKAGHATKVIFLTADAFGVLPPVSRLTADQTQYHFLSGFTAKLAGTERGITEPTPTFSACFGAAFLSLHPTQYAEVLVKRMQAAGAQAYLVNTGWNGTGKRISIKDTRAIIDAILNGSLDNAETFTLPMFNLAIPTELPGVDTKILDPRNTYASPEQWQEKAETLAKLFIDNFDKYTDTPAGAALVAAGPKL

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 2 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	339

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6. Citations (1)

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length_a	125.170 Å
length_b	95.680 Å
length_c	46.560 Å
angle_alpha	90.00 °
angle_beta	95.80 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	1.580 Å
resolution_low	21.950 Å
r_factor	0.1665
r_work	0.1659
r_free	0.1853

fit	/app/data/saxs_computation/1k/11ko/11ko.fit
pddf	/app/data/pr_computation/1k/11ko/11ko.pr.out
profile	/app/data/saxs_computation/1k/11ko/11ko.dat