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9tpm

Structure of LolB from Porphyromonas gingivalis

Method: X-RAY DIFFRACTION D_max: 63.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9tpm
deposition_date	2025-12-18
title	Structure of LolB from Porphyromonas gingivalis
keywords	lipoprotein transport, insertase, lipoprotein, LIPID BINDING PROTEIN; LIPID 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	19.69 Å
rg_electron	18.37 Å
i0	13847300.00
molecular_weight	28059.0 kDa
excluded_volume	35286 Å³
envelope_volume	42402 Å³
shell_volume	19267 Å³
envelope_diameter	64.5 Å
shell_rg	24.60 Å
envelope_rg	18.49 Å
shape_rg	18.34 Å
total_rg	19.43 Å
total_atoms	2082
n_residues	236
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	63.3 Å
rg_real	19.55 Å
rg_real_error	0.30 Å
i0_real	1.3850e+07
i0_real_error	1.6690e+05
rg_reciprocal	19.57 Å
i0_reciprocal	13850000.0000
total_estimate	0.8854
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.8 Å
skewness	0.124
kurtosis	-0.321
angular_range	— – 0.4050 Å⁻¹
current_alpha	0.0000
highest_alpha	1772000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.838; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.995

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	DUF4292 domain-containing protein
formula_weight	31115.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2160

MKHHHHHHPMSDYDIPTTENLYFQGAMGNDMEVSSPAALFANIKEHYPRQDRFSATGKAILRFDQKEVNTRIELTLVRNRGIRLVAMPFPLVVAGRAWITPEGMTVTDAINKRYVTASYSQLSELTGIELSYRAFESLFLAQLFKADGASIVASDLLLSTGAQKGHLLSYQDNRKMEYISEIGSNRRPLSISIYDPSTHYRLATTYSSFRKYGAEHNLPANLLLQVLHLGQVKGSLSLDLPKMRFTDIDETDVTPRVNTSTYRRMTLEDLSELF

Source

organism	Porphyromonas gingivalis A7A1-28
ncbi_taxonomy_id	1403338
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	5

Entity 5 non-polymer

description	1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE
formula_weight	162.2 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	78

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6. Citations (1)

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length_a	94.679 Å
length_b	94.679 Å
length_c	104.942 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 65 2 2
int_tables_number	179
crystal_system	hexagonal

resolution	2.100 Å
resolution_low	47.340 Å
r_factor	0.2295
r_work	0.2270
r_free	0.2778

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