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9qpn

BtuJ1 (BT_1491) bound to dicyanocobinamide

Method: X-RAY DIFFRACTION D_max: 60.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qpn
deposition_date	2025-03-27
title	BtuJ1 (BT_1491) bound to dicyanocobinamide
keywords	surface-exposed lipoprotein, Corrinoid-binding protein, MEMBRANE PROTEIN; MEMBRANE PROTEIN
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	18.54 Å
rg_electron	17.29 Å
i0	12793200.00
molecular_weight	26702.0 kDa
excluded_volume	33303 Å³
envelope_volume	37770 Å³
shell_volume	18011 Å³
envelope_diameter	62.0 Å
shell_rg	23.79 Å
envelope_rg	17.77 Å
shape_rg	17.25 Å
total_rg	18.42 Å
total_atoms	3658
n_residues	228
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	60.7 Å
rg_real	18.44 Å
rg_real_error	0.35 Å
i0_real	1.2790e+07
i0_real_error	1.4790e+05
rg_reciprocal	18.45 Å
i0_reciprocal	12790000.0000
total_estimate	0.8083
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	23.3 Å
skewness	0.170
kurtosis	-0.383
angular_range	— – 0.4300 Å⁻¹
current_alpha	0.0000
highest_alpha	2684000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.835; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	DUF4465 domain-containing protein
formula_weight	27658.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3805

MGSDDDEKMEVVISFENQLTEAESEFKTDLGEKGEVYFKYEISDPQKMIQLSHYYGDWGFGGGFTYTNKTDVKTPGYSNLSAITGKGKNGKVYLTSNTNSFTPAQITNLNTSKYNFKGAWVTNTTYDYLAIKDGNDGAGDYSIIKGPFSNKDNDWLKLTATGYKADGSKIGSIDFYLADFRNNKQEIVNTWQWFDWSGIKEADYITFEMSSTDNNDNGQMNTPSYFCLDGITLIEKLEHHHHHH

Source

organism	Bacteroides thetaiotaomicron VPI-5482
ncbi_taxonomy_id	226186
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

description	COB(II)INAMIDE
formula_weight	990.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	CYANIDE ION
formula_weight	26.0 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	147

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6. Citations (2)

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length_a	40.380 Å
length_b	51.570 Å
length_c	115.440 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 2 21 21
int_tables_number	18
crystal_system	orthorhombic

resolution	1.470 Å
resolution_low	57.720 Å
r_factor	0.1817
r_work	0.1810
r_free	0.1917

fit	/app/data/saxs_computation/qp/9qpn/9qpn.fit
pddf	/app/data/pr_computation/qp/9qpn/9qpn.pr.out
profile	/app/data/saxs_computation/qp/9qpn/9qpn.dat

BtuJ1 (BT_1491) bound to dicyanocobinamide

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