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9s7k

INCYPRO crosslinked dimer of the D-stereospecific hydrolase dHy1

Method: X-RAY DIFFRACTION D_max: 85.8 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s7k
deposition_date	2025-08-04
title	INCYPRO crosslinked dimer of the D-stereospecific hydrolase dHy1
keywords	stabilization, cyclization, multimer, crosslink, 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	27.73 Å
rg_electron	26.76 Å
i0	88924600.00
molecular_weight	74489.0 kDa
excluded_volume	93545 Å³
envelope_volume	111460 Å³
shell_volume	34144 Å³
envelope_diameter	89.4 Å
shell_rg	34.71 Å
envelope_rg	26.80 Å
shape_rg	26.76 Å
total_rg	27.58 Å
total_atoms	5248
n_residues	678
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	85.8 Å
rg_real	27.65 Å
rg_real_error	0.49 Å
i0_real	8.8920e+07
i0_real_error	1.2210e+06
rg_reciprocal	27.68 Å
i0_reciprocal	88930000.0000
total_estimate	0.9067
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	33.1 Å
skewness	0.264
kurtosis	-0.501
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	30730000.0000
n_real_points	58
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.943; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.953

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	D-alanyl-D-alanine carboxypeptidase
formula_weight	36901.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5406

QSDRTSVKKAIRDELQLGYPGILAQISKGGKTWSYTAGIADLRTKKPMKADFRFRIGSVTKTFIATVLLQLSGENRLNLDDSIEKWLPGVIQGNGYDGNQITIRQILNHTSGIADYINSKDFDIMDTCKSYTAEEFVKMGISLPPDFAPGKGWSYSNTGYVLLGILIEKVTGNSYAEEVENRIIEPLDLSNTFLPGCSSVIPGTKHARGYLQLDGASELKDVTCINPGSSDGDMISTADDLNKFFSYLLGGKLLKEQQLKQMLTTVPTNREGTGYGLGILEIKLPNGVSVWGHRGGVLGFSTFAGGTLGGKHTLAINSNSFNINNPESFKNVLIAEFSK

Source

organism	Bacillus thuringiensis
ncbi_taxonomy_id	1428
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	N-[2-[3,5-bis[2-(2-iodanylethanoylamino)ethanoyl]-1,3,5-triazinan-1-yl]-2-oxidanylidene-ethyl]-2-iodanyl-ethanamide
formula_weight	762.1 kDa
src_method	syn
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	157

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6. Citations (1)

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length_a	53.776 Å
length_b	53.764 Å
length_c	57.373 Å
angle_alpha	75.69 °
angle_beta	75.69 °
angle_gamma	87.81 °
z_pdb	2

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	1.771 Å
resolution_low	43.115 Å
r_factor	—
r_work	0.2399
r_free	0.2696

fit	/app/data/saxs_computation/s7/9s7k/9s7k.fit
pddf	/app/data/pr_computation/s7/9s7k/9s7k.pr.out
profile	/app/data/saxs_computation/s7/9s7k/9s7k.dat

INCYPRO crosslinked dimer of the D-stereospecific hydrolase dHy1

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