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9qnp

Streptavidin K121W with a thiophenol cofactor as artificial hydrogen atom transferase

Method: X-RAY DIFFRACTION D_max: 68.4 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qnp
deposition_date	2025-03-25
title	Streptavidin K121W with a thiophenol cofactor as artificial hydrogen atom transferase
keywords	Hydrogen atom transfer, thiophenol, streptavidin, transferase; TRANSFERASE
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	22.62 Å
rg_electron	21.70 Å
i0	96364900.00
molecular_weight	50913.0 kDa
excluded_volume	48763 Å³
envelope_volume	76765 Å³
shell_volume	28186 Å³
envelope_diameter	71.2 Å
shell_rg	29.40 Å
envelope_rg	21.97 Å
shape_rg	21.67 Å
total_rg	22.35 Å
total_atoms	3859
n_residues	501
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	68.4 Å
rg_real	22.47 Å
rg_real_error	0.32 Å
i0_real	9.6360e+07
i0_real_error	1.2720e+06
rg_reciprocal	22.51 Å
i0_reciprocal	96370000.0000
total_estimate	0.9065
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	29.0 Å
skewness	0.102
kurtosis	-0.548
angular_range	— – 0.3500 Å⁻¹
current_alpha	0.0000
highest_alpha	26940000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.939; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.982

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Streptavidin
formula_weight	16626.1 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	3940

MASMTGGQQMGRDQAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWWSTLVGHDTFTKVKPSAASIDAAKKAGVNNGNPLDAVQQ

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	4

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	81

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6. Citations (1)

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length_a	115.245 Å
length_b	89.026 Å
length_c	57.891 Å
angle_alpha	90.00 °
angle_beta	96.90 °
angle_gamma	90.00 °
z_pdb	16

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.300 Å
resolution_low	43.220 Å
r_factor	0.2001
r_work	0.1974
r_free	0.2539

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

Streptavidin K121W 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