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9qo7

Streptavidin K121M with a thiophenol cofactor as artificial hydrogen atom transferase

Method: X-RAY DIFFRACTION D_max: 52.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qo7
deposition_date	2025-03-25
last_revision	2026-04-08
title	Streptavidin K121M 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	15.79 Å
rg_electron	14.93 Å
i0	6817260.00
molecular_weight	12612.0 kDa
excluded_volume	12043 Å³
envelope_volume	19014 Å³
shell_volume	11360 Å³
envelope_diameter	53.1 Å
shell_rg	19.90 Å
envelope_rg	15.52 Å
shape_rg	14.87 Å
total_rg	15.74 Å
total_atoms	954
n_residues	124
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	52.9 Å
rg_real	15.81 Å
rg_real_error	0.34 Å
i0_real	6.8170e+06
i0_real_error	8.5430e+04
rg_reciprocal	15.81 Å
i0_reciprocal	6817000.0000
total_estimate	0.8027
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	18.1 Å
skewness	0.417
kurtosis	-0.208
angular_range	— – 0.5000 Å⁻¹
current_alpha	0.0000
highest_alpha	952100.0000
n_real_points	80
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.828; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.949; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Streptavidin
formula_weight	16571.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	983

MASMTGGQQMGRDQAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWMSTLVGHDTFTKVKPSAASIDAAKKAGVNNGNPLDAVQQ

Source

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

Entity 2 non-polymer

description	;~{N}-[4-[(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]butyl]-3-sulfanyl-benzamide ;
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	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	22

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6. Citations (1)

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length_a	57.832 Å
length_b	57.832 Å
length_c	77.739 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 42 21 2
int_tables_number	94
crystal_system	—

resolution	2.000 Å
resolution_low	40.890 Å
r_factor	0.2272
r_work	0.2248
r_free	0.2776

fit	/app/data/saxs_computation/qo/9qo7/9qo7.fit
pddf	/app/data/pr_computation/qo/9qo7/9qo7.pr.out
profile	/app/data/saxs_computation/qo/9qo7/9qo7.dat

Streptavidin K121M 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