← Back to search

9qne

Streptavidin with a thiophenol cofactor as artificial hydrogen atom transferase

Method: X-RAY DIFFRACTION D_max: 54.7 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9qne
deposition_date	2025-03-24
title	Streptavidin with a thiophenol cofactor as artificial hydrogen atom transferase
keywords	Hydrogen atom transfer, thiophenol, streptavidin, TRANSFERASE; TRANSFERASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	15.97 Å
rg_electron	15.05 Å
i0	7256520.00
molecular_weight	13008.0 kDa
excluded_volume	12414 Å³
envelope_volume	19747 Å³
shell_volume	11639 Å³
envelope_diameter	53.9 Å
shell_rg	20.25 Å
envelope_rg	15.70 Å
shape_rg	15.00 Å
total_rg	15.89 Å
total_atoms	983
n_residues	125
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

▼

3. P(r) Analysis (GNOM)

dmax	54.7 Å
rg_real	15.99 Å
rg_real_error	0.32 Å
i0_real	7.2570e+06
i0_real_error	8.1580e+04
rg_reciprocal	15.99 Å
i0_reciprocal	7257000.0000
total_estimate	0.6962
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	18.0 Å
skewness	0.427
kurtosis	-0.195
angular_range	— – 0.5000 Å⁻¹
current_alpha	0.0000
highest_alpha	1164000.0000
n_real_points	80
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.788; Stabil: 1.000; Sysdev: 0.256; Positv: 1.000; Valcen: 0.926; Smooth: 0.989

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	Streptavidin
formula_weight	16569.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	1125

MASMTGGQQMGRDQAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKPSAASIDAAKKAGVNNGNPLDAVQQ

Source

organism	Streptomyces avidinii
ncbi_taxonomy_id	1895
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	;5-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-(3-sulfanylphenyl)pentanamide ;
formula_weight	351.5 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	6

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	95

▶

6. Citations (1)

▶

length_a	57.388 Å
length_b	57.388 Å
length_c	182.440 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	I 41 2 2
int_tables_number	98
crystal_system	—

resolution	1.840 Å
resolution_low	41.740 Å
r_factor	0.1671
r_work	0.1652
r_free	0.2016

fit	/app/data/saxs_computation/qn/9qne/9qne.fit
pddf	/app/data/pr_computation/qn/9qne/9qne.pr.out
profile	/app/data/saxs_computation/qn/9qne/9qne.dat

Streptavidin with a thiophenol cofactor as artificial hydrogen atom transferase

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