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9rv7

Streptococcus pneumoniae StkP catalytic domain T167A/T169A double mutant in complex with AMP-PNP and Mg2+

Method: X-RAY DIFFRACTION D_max: 82.9 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rv7
deposition_date	2025-07-07
last_revision	2026-06-10
title	Streptococcus pneumoniae StkP catalytic domain T167A/T169A double mutant in complex with AMP-PNP and Mg2+
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	26.07 Å
rg_electron	25.16 Å
i0	63802900.00
molecular_weight	61629.0 kDa
excluded_volume	77021 Å³
envelope_volume	91899 Å³
shell_volume	30194 Å³
envelope_diameter	88.6 Å
shell_rg	32.66 Å
envelope_rg	25.44 Å
shape_rg	25.18 Å
total_rg	25.91 Å
total_atoms	4509
n_residues	542
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	82.9 Å
rg_real	25.98 Å
rg_real_error	0.49 Å
i0_real	6.3800e+07
i0_real_error	9.0930e+05
rg_reciprocal	26.01 Å
i0_reciprocal	63800000.0000
total_estimate	0.6980
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	29.9 Å
skewness	0.225
kurtosis	-0.498
angular_range	— – 0.3050 Å⁻¹
current_alpha	0.0000
highest_alpha	14940000.0000
n_real_points	62
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 0.105; Positv: 1.000; Valcen: 1.000; Smooth: 0.980

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Serine/threonine-protein kinase StkP
formula_weight	34570.4 kDa
ec_number	2.7.11.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4888

MGGHHHHHHHGGGRENLYFQGHMIQIGKIFAGRYRIVKQIGRGGMADVYLAKDLILDGEEVAVKVLRTNYQTDPIAVARFQREARAMADLDHPHIVRITDIGEEDGQQYLAMEYVAGLDLKRYIKEHYPLSNEEAVRIMGQILLAMRLAHTRGIVHRDLKPQNILLTPDGTAKVTDFGIAVAFAETSLAQANSMLGSVHYLSPEQARGSKATVQSDIYAMGIIFYEMLTGHIPYDGDSAVTIALQHFQNPLPSVIAENSSVPQALENVIIKATAKKLTNRYRSVSEMYVDLSSSLSYNRRNESKLIFDE

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	2

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	(4S)-2-METHYL-2,4-PENTANEDIOL
formula_weight	118.2 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	379

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6. Citations (1)

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length_a	69.280 Å
length_b	51.730 Å
length_c	81.140 Å
angle_alpha	90.00 °
angle_beta	103.77 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.800 Å
resolution_low	39.400 Å
r_factor	0.1926
r_work	0.1902
r_free	0.2380

fit	/app/data/saxs_computation/rv/9rv7/9rv7.fit
pddf	/app/data/pr_computation/rv/9rv7/9rv7.pr.out
profile	/app/data/saxs_computation/rv/9rv7/9rv7.dat