SAXSdb — 9s6c

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1. Structure Basics

entry_id	9s6c
deposition_date	2025-07-31
last_revision	2025-09-17
title	B12 Binding protein - BtuK1
keywords	Lipoprotein, B12 binding, 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	33.15 Å
rg_electron	32.22 Å
i0	205374000.00
molecular_weight	116450.0 kDa
excluded_volume	145980 Å³
envelope_volume	180330 Å³
shell_volume	45861 Å³
envelope_diameter	102.4 Å
shell_rg	39.94 Å
envelope_rg	31.63 Å
shape_rg	32.24 Å
total_rg	32.75 Å
total_atoms	15800
n_residues	1013
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	100.2 Å
rg_real	32.93 Å
rg_real_error	0.68 Å
i0_real	2.0540e+08
i0_real_error	3.0330e+06
rg_reciprocal	33.03 Å
i0_reciprocal	205400000.0000
total_estimate	0.9119
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	39.7 Å
skewness	0.071
kurtosis	-0.718
angular_range	— – 0.2400 Å⁻¹
current_alpha	0.0000
highest_alpha	40700000.0000
n_real_points	49
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.964; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.962

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Quinoprotein amine dehydrogenase-like protein
formula_weight	37401.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C
atom_count	16442

GKGCLIINEGWFGHGSGSISFYNYEKNSIEHWCYKNQNFGDVLGVTSQSATLWNGKLYVCSKEDNQLVVMDPKTLYAENSCGKLANYQAYEFIGLNDDYGIITHGGYFSRINLKTFETITLVSVGNTYTGTGSGIAYNGKLILNVNSSGWGSPKVYTIDIAELCSPDLKPTDKVAFQELDIATYGGTRFVQCKDGNIYTVETTKDGKNNLVRINADFSLKKVAMRDDYSPSSFGAYREASFCGTPEGIFYYIAGGKIYKATFDNPAPEETLTEYTKEGYGFYGAGIRVNPKTNELLAMYLTGDYQKNLLVRFNAATGEKISEIAYDGYYFPATFIFN

Source

organism	Bacteroides thetaiotaomicron
ncbi_taxonomy_id	818
host_organism	Escherichia coli

Entity 2 polymer

description	Quinoprotein amine dehydrogenase-like protein
formula_weight	37671.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B

GHMKGCLIINEGWFGHGSGSISFYNYEKNSIEHWCYKNQNFGDVLGVTSQSATLWNGKLYVCSKEDNQLVVMDPKTLYAENSCGKLANYQAYEFIGLNDDYGIITHGGYFSRINLKTFETITLVSVGNTYTGTGSGIAYNGKLILNVNSSGWGSPKVYTIDIAELCSPDLKPTDKVAFQELDIATYGGTRFVQCKDGNIYTVETTKDGKNNLVRINADFSLKKVAMRDDYSPSSFGAYREASFCGTPEGIFYYIAGGKIYKATFDNPAPEETLTEYTKEGYGFYGAGIRVNPKTNELLAMYLTGDYQKNLLVRFNAATGEKISEIAYDGYYFPATFIFN

Source

organism	Bacteroides thetaiotaomicron
ncbi_taxonomy_id	818
host_organism	Escherichia coli

Entity 3 non-polymer

description	CYANOCOBALAMIN
formula_weight	1356.4 kDa
src_method	syn
entity_count	3

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	642

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6. Citations (1)

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length_a	52.739 Å
length_b	129.984 Å
length_c	164.660 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.817 Å
resolution_low	14.287 Å
r_factor	—
r_work	0.1625
r_free	0.1917

fit	/app/data/saxs_computation/s6/9s6c/9s6c.fit
pddf	/app/data/pr_computation/s6/9s6c/9s6c.pr.out
profile	/app/data/saxs_computation/s6/9s6c/9s6c.dat

B12 Binding protein - BtuK1

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

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)