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9r6u

Crystal structure of E. coli Adenylate kinase K47A mutant in complex with inhibitor Ap5A

Method: X-RAY DIFFRACTION D_max: 81.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r6u
deposition_date	2025-05-13
title	Crystal structure of E. coli Adenylate kinase K47A mutant in complex with inhibitor Ap5A
keywords	ADENYLATE KINASE, K47A mutant, AP5A, PROTEIN DYNAMICS, TRANSFERASE; TRANSFERASE
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	26.14 Å
rg_electron	25.60 Å
i0	43411400.00
molecular_weight	48996.0 kDa
excluded_volume	60592 Å³
envelope_volume	76791 Å³
shell_volume	25460 Å³
envelope_diameter	83.6 Å
shell_rg	32.36 Å
envelope_rg	25.35 Å
shape_rg	25.61 Å
total_rg	26.34 Å
total_atoms	3425
n_residues	428
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	81.1 Å
rg_real	26.20 Å
rg_real_error	0.53 Å
i0_real	4.3410e+07
i0_real_error	5.0590e+05
rg_reciprocal	26.18 Å
i0_reciprocal	43410000.0000
total_estimate	0.8910
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.2 Å
skewness	0.341
kurtosis	-0.616
angular_range	— – 0.3050 Å⁻¹
current_alpha	0.0000
highest_alpha	9171000.0000
n_real_points	62
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.954; Smooth: 0.847

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Adenylate kinase
formula_weight	23561.9 kDa
ec_number	2.7.4.3
mutation	K47A
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3949

MRIILLGAPGAGKGTQAQFIMEKYGIPQISTGDMLRAAVKSGSELGAQAKDIMDAGKLVTDELVIALVKERIAQEDCRNGFLLDGFPRTIPQADAMKEAGINVDYVLEFDVPDELIVDRIVGRRVHAPSGRVYHVKFNPPKVEGKDDVTGEELTTRKDDQEETVRKRLVEYHQMTAPLIGYYSKEAEAGNTKYAKVDGTKPVAEVRADLEKILG

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 2 non-polymer

description	BIS(ADENOSINE)-5'-PENTAPHOSPHATE
formula_weight	916.4 kDa
src_method	nat
entity_count	2

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	nat
entity_count	1

Entity 4 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	nat
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	401

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6. Citations (1)

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length_a	73.763 Å
length_b	79.057 Å
length_c	83.115 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 2 21
int_tables_number	18
crystal_system	—

resolution	1.770 Å
resolution_low	45.240 Å
r_factor	—
r_work	0.1919
r_free	0.2279

fit	/app/data/saxs_computation/r6/9r6u/9r6u.fit
pddf	/app/data/pr_computation/r6/9r6u/9r6u.pr.out
profile	/app/data/saxs_computation/r6/9r6u/9r6u.dat