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9qr5

InlB392_V333E: V333E variant of Listeria monocytogenes InlB (internalin B) residues 36-392

Method: X-RAY DIFFRACTION D_max: 103.3 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qr5
deposition_date	2025-04-03
title	InlB392_V333E: V333E variant of Listeria monocytogenes InlB (internalin B) residues 36-392
keywords	LEUCINE RICH REPEAT, PROTEIN BINDING, PATHOGENICITY, VIRULENCE FACTOR, CELL INVASION; CELL INVASION
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	31.11 Å
rg_electron	31.21 Å
i0	24794800.00
molecular_weight	40148.0 kDa
excluded_volume	50867 Å³
envelope_volume	67759 Å³
shell_volume	20241 Å³
envelope_diameter	111.0 Å
shell_rg	33.76 Å
envelope_rg	31.54 Å
shape_rg	31.24 Å
total_rg	31.36 Å
total_atoms	5709
n_residues	356
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	103.3 Å
rg_real	31.53 Å
rg_real_error	1.14 Å
i0_real	2.4790e+07
i0_real_error	4.1320e+05
rg_reciprocal	31.36 Å
i0_reciprocal	24790000.0000
total_estimate	0.5422
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	22.3 Å
skewness	0.473
kurtosis	-0.587
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	3608000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.661; Stabil: 0.999; Sysdev: 0.115; Positv: 1.000; Valcen: 0.322; Smooth: 0.397

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Internalin B
formula_weight	40451.8 kDa
mutation	V333E
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6462

GPLGSETITVPTPIKQIFSDDAFAETIKDNLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVTKLFLNGNKLTDIKPLANLKNLGWLFLDENKVKDLSSLKDLKKLKSLSLEHNGISDINGLVHLPQLESLYLGNNKITDITVLSRLTKLDTLSLEDNQISDIVPLAGLTKLQNLYLSKNHISDLRALAGLKNLDVLELFSQECLNKPINHQSNLVVPNTVKNTDGSLVTPEIISDDGDYEKPNVKWHLPEFTNEVSFIFYQPVTIGKAKARFHGRVTQPLKEVYTVSYDVDGTEIKTKVEAGTRITAPKPPTKQGYVFKGWYTEKNGGHEWNFNTDYMSGNDFTLYAVFKAET

Source

organism	Listeria monocytogenes EGD-e
ncbi_taxonomy_id	169963
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	569

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6. Citations (1)

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length_a	41.410 Å
length_b	90.770 Å
length_c	99.120 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	1.450 Å
resolution_low	45.380 Å
r_factor	0.1562
r_work	0.1550
r_free	0.1787

fit	/app/data/saxs_computation/qr/9qr5/9qr5.fit
pddf	/app/data/pr_computation/qr/9qr5/9qr5.pr.out
profile	/app/data/saxs_computation/qr/9qr5/9qr5.dat

InlB392_V333E: V333E variant of Listeria monocytogenes InlB (internalin B) residues 36-392

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