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9vak

Carbohydrate-binding module 32 of LnbB from Bifidobacterium bifidum, LNB complex

Method: X-RAY DIFFRACTION D_max: 96.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vak
deposition_date	2025-06-03
title	Carbohydrate-binding module 32 of LnbB from Bifidobacterium bifidum, LNB complex
keywords	Carbohydrate Binding Module Family 32 domain, SUGAR BINDING PROTEIN; SUGAR BINDING 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	28.75 Å
rg_electron	28.17 Å
i0	81770800.00
molecular_weight	70393.0 kDa
excluded_volume	87659 Å³
envelope_volume	110060 Å³
shell_volume	33209 Å³
envelope_diameter	101.3 Å
shell_rg	34.74 Å
envelope_rg	28.06 Å
shape_rg	28.14 Å
total_rg	28.91 Å
total_atoms	4980
n_residues	648
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	96.3 Å
rg_real	28.77 Å
rg_real_error	0.71 Å
i0_real	8.1770e+07
i0_real_error	1.1910e+06
rg_reciprocal	28.76 Å
i0_reciprocal	81770000.0000
total_estimate	0.8796
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.3 Å
skewness	0.406
kurtosis	-0.176
angular_range	— – 0.2750 Å⁻¹
current_alpha	0.0000
highest_alpha	15060000.0000
n_real_points	56
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.844; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.927

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Lacto-N-biosidase
formula_weight	19445.3 kDa
ec_number	3.2.1.140
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	B,A,C,D
atom_count	5360

MGSSHHHHHHSSGLVPRGSSLTKDVEASDYAASSQETTGEHAPVGNAFDKNANTFWHSKYSNPSANLPHWLAFKASPGEGNKIAAITHLYRQDKLNGPAKNVAVYVVAASDANSVADVTNWGEPVATAEFPYTKELQTIALPNTIPSGDVYVKFQINDAWGLTETSAGVTWAAVAELAATAKA

Source

organism	Bifidobacterium bifidum JCM 1254
ncbi_taxonomy_id	398514
host_organism	Escherichia coli BL21(DE3)

Entity 2 branched

description	beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	383.3 kDa
src_method	man
entity_count	4

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	4

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	380

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6. Citations (2)

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length_a	56.489 Å
length_b	105.802 Å
length_c	122.102 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 2 21 21
int_tables_number	18
crystal_system	—

resolution	2.000 Å
resolution_low	48.540 Å
r_factor	0.1997
r_work	0.1981
r_free	0.2296

fit	/app/data/saxs_computation/va/9vak/9vak.fit
pddf	/app/data/pr_computation/va/9vak/9vak.pr.out
profile	/app/data/saxs_computation/va/9vak/9vak.dat

Carbohydrate-binding module 32 of LnbB from Bifidobacterium bifidum, LNB complex

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