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9qdi

Crystal structure of BF3526 peptidase from Bacteroides fragilis in complex with a peptide

Method: X-RAY DIFFRACTION D_max: 151.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qdi
deposition_date	2025-03-06
title	Crystal structure of BF3526 peptidase from Bacteroides fragilis in complex with a peptide
keywords	;IgA protease, peptidase, protease, BF3526, M64, metallopeptidase, metalloprotease, antibody, Ig, IgA, Bacteroides, metzincin, nephropathy, IgAN, hinge, complex, substrate, product, HYDROLASE ;; HYDROLASE
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	49.20 Å
rg_electron	48.53 Å
i0	1888790000.00
molecular_weight	367730.0 kDa
excluded_volume	461060 Å³
envelope_volume	637550 Å³
shell_volume	105120 Å³
envelope_diameter	157.7 Å
shell_rg	56.83 Å
envelope_rg	46.79 Å
shape_rg	48.53 Å
total_rg	48.82 Å
total_atoms	41658
n_residues	3234
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	151.1 Å
rg_real	48.74 Å
rg_real_error	0.87 Å
i0_real	1.8890e+09
i0_real_error	3.2400e+07
rg_reciprocal	49.20 Å
i0_reciprocal	1890000000.0000
total_estimate	0.8737
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	66.1 Å
skewness	0.009
kurtosis	-0.444
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	261100000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.856; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.830

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

Entity 1 polymer

description	Lipoprotein
formula_weight	46148.8 kDa
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H
atom_count	43108

GAQNFSDYFTNKTLRIDYLFTGNADKQSICLDELSELPVWAGRRHHLSELPLEGNGQIVMRDVASGKVIYTTSFSSLFQEWLETDEAKEVTKGFENTYLLPYPIKPAEVEITLRNNKREVSANLKHVVKPDDILIHKKGLTHITPHKYLLKSGNEEQCIDVAILAEGYTTSEMETFYKDAAIACEALFSHEPFQSMKNRFNIVAVASPSADSGVSAPKQGAWKHTAFGSHFDTFYSDRYLTTSRVKAINDALAGIPYEHIIILANTEQYGGGGIYNAFTLTTAHHPNFRPVVVHEFGHSFGGLADEYFYDEDVMNGLYPLNIEPWEQNITTRINFASKWEDMLTKTTPVPTPVADKAKYPIGVYEGGGYSAKGIYRPAFDCRMRTNEYPTFCPVCQRAIQRIIEFYTGK

Source

organism	Bacteroides fragilis NCTC 9343
ncbi_taxonomy_id	272559
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Synthetic peptide SER-THR-PRO-PRO
formula_weight	400.4 kDa
src_method	syn
entity_count	4

Polymer

type	polypeptide(L)
strand_id	I,J,K,L

STPP

Entity 3 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	8

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	16

Entity 5 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	15

Entity 6 non-polymer

description	N-PROPANOL
formula_weight	60.1 kDa
src_method	syn
entity_count	5

Entity 7 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 8 non-polymer

description	1,4-BUTANEDIOL
formula_weight	90.1 kDa
src_method	syn
entity_count	1

Entity 9 non-polymer

description	HEXANE-1,6-DIOL
formula_weight	118.2 kDa
src_method	syn
entity_count	1

Entity 10 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1372

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6. Citations (1)

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length_a	99.294 Å
length_b	99.435 Å
length_c	103.386 Å
angle_alpha	74.16 °
angle_beta	88.13 °
angle_gamma	82.44 °
z_pdb	8

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	1.940 Å
resolution_low	29.640 Å
r_factor	0.1729
r_work	0.1709
r_free	0.2127

fit	/app/data/saxs_computation/qd/9qdi/9qdi.fit
pddf	/app/data/pr_computation/qd/9qdi/9qdi.pr.out
profile	/app/data/saxs_computation/qd/9qdi/9qdi.dat

Crystal structure of BF3526 peptidase from Bacteroides fragilis in complex with a peptide

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

5. Entities & Polymer Info (10)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)