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9qr4

InlB392_T336Y: T336Y variant of Listeria monocytogenes InlB (internalin B) residues 36-392

Method: X-RAY DIFFRACTION D_max: 172.7 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qr4
deposition_date	2025-04-03
title	InlB392_T336Y: T336Y 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	46.17 Å
rg_electron	46.71 Å
i0	205752000.00
molecular_weight	121060.0 kDa
excluded_volume	153520 Å³
envelope_volume	231100 Å³
shell_volume	46003 Å³
envelope_diameter	166.6 Å
shell_rg	43.81 Å
envelope_rg	47.37 Å
shape_rg	46.82 Å
total_rg	46.15 Å
total_atoms	17229
n_residues	1072
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	172.7 Å
rg_real	46.76 Å
rg_real_error	2.55 Å
i0_real	2.0580e+08
i0_real_error	4.3410e+06
rg_reciprocal	46.18 Å
i0_reciprocal	205600000.0000
total_estimate	0.7460
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	55.9 Å
skewness	0.598
kurtosis	-0.035
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	9234000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.620; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.834; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Internalin B
formula_weight	40483.9 kDa
mutation	T336Y
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	19082

GPLGSETITVPTPIKQIFSDDAFAETIKDNLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVTKLFLNGNKLTDIKPLANLKNLGWLFLDENKVKDLSSLKDLKKLKSLSLEHNGISDINGLVHLPQLESLYLGNNKITDITVLSRLTKLDTLSLEDNQISDIVPLAGLTKLQNLYLSKNHISDLRALAGLKNLDVLELFSQECLNKPINHQSNLVVPNTVKNTDGSLVTPEIISDDGDYEKPNVKWHLPEFTNEVSFIFYQPVTIGKAKARFHGRVTQPLKEVYTVSYDVDGTVIKYKVEAGTRITAPKPPTKQGYVFKGWYTEKNGGHEWNFNTDYMSGNDFTLYAVFKAET

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	11

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1405

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6. Citations (1)

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length_a	44.920 Å
length_b	149.170 Å
length_c	220.810 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	12

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	1.600 Å
resolution_low	20.130 Å
r_factor	0.1740
r_work	0.1728
r_free	0.1959

fit	/app/data/saxs_computation/qr/9qr4/9qr4.fit
pddf	/app/data/pr_computation/qr/9qr4/9qr4.pr.out
profile	/app/data/saxs_computation/qr/9qr4/9qr4.dat

InlB392_T336Y: T336Y 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