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9qfr

Crystal structure of Def1 in complex with actinonin

Method: X-RAY DIFFRACTION D_max: 91.9 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qfr
deposition_date	2025-03-12
title	Crystal structure of Def1 in complex with actinonin
keywords	metalloprotease, antibiotic, protein translation, 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	24.60 Å
rg_electron	24.45 Å
i0	25250600.00
molecular_weight	38640.0 kDa
excluded_volume	48482 Å³
envelope_volume	58619 Å³
shell_volume	21574 Å³
envelope_diameter	94.4 Å
shell_rg	29.47 Å
envelope_rg	25.00 Å
shape_rg	24.47 Å
total_rg	24.98 Å
total_atoms	2708
n_residues	336
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	91.9 Å
rg_real	24.91 Å
rg_real_error	0.87 Å
i0_real	2.5250e+07
i0_real_error	3.9030e+05
rg_reciprocal	24.84 Å
i0_reciprocal	25250000.0000
total_estimate	0.5686
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	23.3 Å
skewness	0.671
kurtosis	0.130
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	5479000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.533; Stabil: 1.000; Sysdev: 0.137; Positv: 1.000; Valcen: 0.503; Smooth: 0.876

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Peptide deformylase 1
formula_weight	20433.3 kDa
ec_number	3.5.1.88
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3144

MHHHHHHGSGSGSSVLQVLTFPDDRLRTVAKPVEQVTPEIQQIVDDMLETMYAEEGIGLAATQVDIHQRIVVIDISETRDQPMVLINPEIIEKRGEDGIEEGCLSVPGARALVPRAAEVTVKALDRNGQEYQFDADDLLAICVQHELDHLAGKLFVDYLSPLKRNRIKEKLEKIKRFNEKK

Source

organism	Vibrio cholerae O1 biovar El Tor str. N16961
ncbi_taxonomy_id	243277
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	NICKEL (II) ION
formula_weight	58.7 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	ACTINONIN
formula_weight	385.5 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	430

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6. Citations (1)

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length_a	41.780 Å
length_b	44.480 Å
length_c	213.660 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	1.520 Å
resolution_low	41.000 Å
r_factor	0.1764
r_work	0.1750
r_free	0.2057

fit	/app/data/saxs_computation/qf/9qfr/9qfr.fit
pddf	/app/data/pr_computation/qf/9qfr/9qfr.pr.out
profile	/app/data/saxs_computation/qf/9qfr/9qfr.dat

Crystal structure of Def1 in complex with actinonin

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