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9urd

Crystal structure of Zinc-binding metallopeptidase (Uniprot: A0AAN3A8D2) from Bacteroides ovatus

Method: X-RAY DIFFRACTION D_max: 75.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9urd
deposition_date	2025-04-29
last_revision	2026-04-29
title	Crystal structure of Zinc-binding metallopeptidase (Uniprot: A0AAN3A8D2) from Bacteroides ovatus
keywords	endopeptidase, lipoprotein, autoproteolysis, Pfam: PF15890, 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	19.72 Å
rg_electron	18.54 Å
i0	13693400.00
molecular_weight	27779.0 kDa
excluded_volume	34656 Å³
envelope_volume	39760 Å³
shell_volume	18168 Å³
envelope_diameter	77.0 Å
shell_rg	24.57 Å
envelope_rg	19.03 Å
shape_rg	18.52 Å
total_rg	19.47 Å
total_atoms	1962
n_residues	239
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	75.9 Å
rg_real	19.70 Å
rg_real_error	0.70 Å
i0_real	1.3690e+07
i0_real_error	1.9270e+05
rg_reciprocal	19.70 Å
i0_reciprocal	13690000.0000
total_estimate	0.7982
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	23.5 Å
skewness	0.394
kurtosis	0.108
angular_range	— – 0.4050 Å⁻¹
current_alpha	0.0000
highest_alpha	2240000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.511; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.843; Smooth: 0.996

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Substrate import-associated zinc metallohydrolase lipoprotein
formula_weight	38180.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2135

MASWSHPQFEKGSSHHHHHHSSGSGGGGGENLYFQGSKKYIIYSLIITLTCGLGACNNDEGVDKANSIFSTEEVERSPFDNWILGNYTHPYNIALKYRMEDNESDMTHVLAPADYKKSVVLAKIIKHVWLEAYDEATGNPDFLRQYIPKTIHFIGSPAYEDNGTMVLGTAEGGMKITLYNVNDINPDKIDINLLNEYYFQTMHHEFAHILHQTKNYDPAFDRITENAYIGSDWYMVGANRNAWQQGFVTSYAMSESREDFVENIAVYVTNTEDYWNNMLQNAGESGRALIKQKFEIVYSYMEQTWGINLDELRDIVLRRQDDIANGNVDLSIIE

Source

organism	Bacteroides ovatus ATCC 8483
ncbi_taxonomy_id	411476
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	155

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6. Citations (1)

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length_a	42.314 Å
length_b	66.810 Å
length_c	99.072 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	2.100 Å
resolution_low	38.910 Å
r_factor	0.2268
r_work	0.2248
r_free	0.2679

fit	/app/data/saxs_computation/ur/9urd/9urd.fit
pddf	/app/data/pr_computation/ur/9urd/9urd.pr.out
profile	/app/data/saxs_computation/ur/9urd/9urd.dat

Crystal structure of Zinc-binding metallopeptidase (Uniprot: A0AAN3A8D2) from Bacteroides ovatus

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