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9ues

Crystal structure of an inactive TKSP mutant in complex with the TKS propeptide

Method: X-RAY DIFFRACTION D_max: 78.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ues
deposition_date	2025-04-09
last_revision	2026-02-18
title	Crystal structure of an inactive TKSP mutant in complex with the TKS propeptide
keywords	Subtilase, Propeptide, Maturation, Hyperthermophile, HYDROLASE; HYDROLASE
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	23.79 Å
rg_electron	22.86 Å
i0	40746700.00
molecular_weight	49766.0 kDa
excluded_volume	62321 Å³
envelope_volume	70513 Å³
shell_volume	25842 Å³
envelope_diameter	81.0 Å
shell_rg	30.07 Å
envelope_rg	23.37 Å
shape_rg	22.87 Å
total_rg	23.65 Å
total_atoms	3513
n_residues	474
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	78.8 Å
rg_real	23.76 Å
rg_real_error	0.53 Å
i0_real	4.0750e+07
i0_real_error	5.7950e+05
rg_reciprocal	23.77 Å
i0_reciprocal	40750000.0000
total_estimate	0.8811
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.3 Å
skewness	0.332
kurtosis	-0.336
angular_range	— – 0.3350 Å⁻¹
current_alpha	0.0000
highest_alpha	12590000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.844; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.931

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Tk-subtilisin
formula_weight	7644.0 kDa
ec_number	3.4.21.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3513

MGEQNTIRVIVSVDKAKFNPHEVLGIGGHIVYQFKLIPAVVVDVPANAVGKLKKMPGVEKVEFDHQAVLL

Source

organism	Thermococcus kodakarensis KOD1
ncbi_taxonomy_id	69014
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Subtilisin-like serine protease
formula_weight	44352.6 kDa
ec_number	3.4.21.62
mutation	S359A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MVETEGLDESAAQVMATNMWNLGYDGSGITIGIIDTGIDASHPDLQGKVIGWVDFVNGKTTPYDDNGHGTHVASIAAGTGAASNGKYKGMAPGAKLVGIKVLNGQGSGSISDIINGVDWAVQNKDKYGIKVINLSLGSSQSSDGTDSLSQAVNNAWDAGLVVVVAAGNSGPNKYTVGSPAAASKVITVGAVDKYDVITDFSSRGPTADNRLKPEVVAPGNWIIAARASGTSMGQPINDYYTAAPGTAMATPHVAGIAALLLQAHPSWTPDKVKTALIETADIVKPDEIADIAYGAGRVNAYKAAYYDNYAKLTFTGYVSNKGSQSHQFTISGAGFVTATLYWDNSGSDLDLYLYDPNGNQVDYSYTAYYGFEKVGYYNPTAGTWTIKVVSYSGSANYQVDVVSDGSLGQPSGGGSEPSPSPSPEPTV

Source

organism	Thermococcus kodakarensis KOD1
ncbi_taxonomy_id	69014
host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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length_a	136.141 Å
length_b	136.141 Å
length_c	97.985 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 61
int_tables_number	169
crystal_system	—

resolution	3.200 Å
resolution_low	45.240 Å
r_factor	0.2092
r_work	0.2075
r_free	0.2407

fit	/app/data/saxs_computation/ue/9ues/9ues.fit
pddf	/app/data/pr_computation/ue/9ues/9ues.pr.out
profile	/app/data/saxs_computation/ue/9ues/9ues.dat

Crystal structure of an inactive TKSP mutant in complex with the TKS propeptide

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

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)