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9tp6

Structure of LolA3 from Porphyromonas gingivalis

Method: X-RAY DIFFRACTION D_max: 102.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9tp6
deposition_date	2025-12-17
title	Structure of LolA3 from Porphyromonas gingivalis
keywords	lipoprotein transfer, TRANSPORT PROTEIN; TRANSPORT 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	33.08 Å
rg_electron	32.49 Å
i0	119216000.00
molecular_weight	84687.0 kDa
excluded_volume	105250 Å³
envelope_volume	139590 Å³
shell_volume	36465 Å³
envelope_diameter	105.0 Å
shell_rg	38.59 Å
envelope_rg	31.81 Å
shape_rg	32.49 Å
total_rg	33.01 Å
total_atoms	5941
n_residues	719
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	102.6 Å
rg_real	32.99 Å
rg_real_error	0.84 Å
i0_real	1.1920e+08
i0_real_error	1.6910e+06
rg_reciprocal	33.03 Å
i0_reciprocal	119200000.0000
total_estimate	0.8981
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	29.9 Å
skewness	0.121
kurtosis	-0.794
angular_range	— – 0.2400 Å⁻¹
current_alpha	0.0000
highest_alpha	68460000.0000
n_real_points	49
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.950

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Outer membrane lipoprotein-sorting protein
formula_weight	31927.4 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,B,C
atom_count	5948

MHHHHHHGKPIPNPLLGLDSTENLYFQGIDPFTQTGRDIAQRVKDRPDGDTRRSELTMKLINKRGAVRERKLISYSIDMGKDKKDKKTIMFFLYPGDVKGTGFLTWDYDQIGKDDDKWLYLPAMKKTRRISGASAKKDYFMGSDFTYDDMGSRNVDEDTHKLLGEETFDGHKCWKLESTSKDQRDVFSKKIAWIRQDCLIPVRVEYYDRMNRLHRLLELSDIAQIDGFWMAQKMNMSNVQTGHRTVLEIKKPEFNRPIDESKFTVTSLEKGSL

Source

organism	Porphyromonas gingivalis ATCC 33277
ncbi_taxonomy_id	431947
host_organism	Escherichia coli

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	L(+)-TARTARIC ACID
formula_weight	150.1 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	7

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6. Citations (1)

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length_a	124.113 Å
length_b	124.113 Å
length_c	44.389 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	9

space_group	P 32
int_tables_number	145
crystal_system	—

resolution	2.320 Å
resolution_low	41.030 Å
r_factor	0.2393
r_work	0.2368
r_free	0.2866

fit	/app/data/saxs_computation/tp/9tp6/9tp6.fit
pddf	/app/data/pr_computation/tp/9tp6/9tp6.pr.out
profile	/app/data/saxs_computation/tp/9tp6/9tp6.dat

Structure of LolA3 from Porphyromonas gingivalis

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