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9ruj

Streptococcus pneumoniae StkP catalytic domain T167E/T169E double mutant in complex with AMP-PNP and Mn2+

Method: X-RAY DIFFRACTION D_max: 83.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ruj
deposition_date	2025-07-04
last_revision	2026-06-10
title	Streptococcus pneumoniae StkP catalytic domain T167E/T169E double mutant in complex with AMP-PNP and Mn2+
keywords	protein kinase, Streptococcus pneumoniae, bacterial cell division, protein- phosphorylation, StkP, dimerization, CELL CYCLE; CELL CYCLE
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	26.13 Å
rg_electron	25.25 Å
i0	59477300.00
molecular_weight	59908.0 kDa
excluded_volume	75104 Å³
envelope_volume	91140 Å³
shell_volume	29965 Å³
envelope_diameter	86.7 Å
shell_rg	32.55 Å
envelope_rg	25.46 Å
shape_rg	25.28 Å
total_rg	25.99 Å
total_atoms	4212
n_residues	533
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	83.0 Å
rg_real	26.04 Å
rg_real_error	0.44 Å
i0_real	5.9480e+07
i0_real_error	7.2380e+05
rg_reciprocal	26.07 Å
i0_reciprocal	59480000.0000
total_estimate	0.9051
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	81.7 Å
skewness	0.217
kurtosis	-0.492
angular_range	— – 0.3050 Å⁻¹
current_alpha	0.0000
highest_alpha	12030000.0000
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: 1.000; Smooth: 0.983

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Serine/threonine-protein kinase StkP
formula_weight	34686.5 kDa
ec_number	2.7.11.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4516

MGGHHHHHHHGGGRENLYFQGHMIQIGKIFAGRYRIVKQIGRGGMADVYLAKDLILDGEEVAVKVLRTNYQTDPIAVARFQREARAMADLDHPHIVRITDIGEEDGQQYLAMEYVAGLDLKRYIKEHYPLSNEEAVRIMGQILLAMRLAHTRGIVHRDLKPQNILLTPDGTAKVTDFGIAVAFAETSLEQENSMLGSVHYLSPEQARGSKATVQSDIYAMGIIFYEMLTGHIPYDGDSAVTIALQHFQNPLPSVIAENSSVPQALENVIIKATAKKLTNRYRSVSEMYVDLSSSLSYNRRNESKLIFDE

Source

organism	Streptococcus pneumoniae R6
ncbi_taxonomy_id	171101
host_organism	Escherichia coli

Entity 2 non-polymer

description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
formula_weight	506.2 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	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	266

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6. Citations (1)

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length_a	69.433 Å
length_b	51.706 Å
length_c	82.195 Å
angle_alpha	90.00 °
angle_beta	104.49 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.600 Å
resolution_low	45.990 Å
r_factor	0.2088
r_work	0.2081
r_free	0.2334

fit	/app/data/saxs_computation/ru/9ruj/9ruj.fit
pddf	/app/data/pr_computation/ru/9ruj/9ruj.pr.out
profile	/app/data/saxs_computation/ru/9ruj/9ruj.dat

Streptococcus pneumoniae StkP catalytic domain T167E/T169E double mutant in complex with AMP-PNP and Mn2+

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