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9qft

Crystal structure of Def2 in complex with actinonin

Method: X-RAY DIFFRACTION D_max: 83.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qft
deposition_date	2025-03-12
title	Crystal structure of Def2 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	24.88 Å
rg_electron	24.34 Å
i0	23503100.00
molecular_weight	37211.0 kDa
excluded_volume	46789 Å³
envelope_volume	57822 Å³
shell_volume	20772 Å³
envelope_diameter	86.0 Å
shell_rg	30.09 Å
envelope_rg	24.29 Å
shape_rg	24.34 Å
total_rg	25.08 Å
total_atoms	2606
n_residues	328
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	83.4 Å
rg_real	25.03 Å
rg_real_error	0.60 Å
i0_real	2.3500e+07
i0_real_error	3.0070e+05
rg_reciprocal	24.99 Å
i0_reciprocal	23500000.0000
total_estimate	0.8567
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	23.8 Å
skewness	0.411
kurtosis	-0.543
angular_range	— – 0.3200 Å⁻¹
current_alpha	0.0000
highest_alpha	5352000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.791; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.781; Smooth: 0.980

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Peptide deformylase 2
formula_weight	19954.7 kDa
ec_number	3.5.1.88
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	G,D
atom_count	2823

MHHHHHHGSGSGSAVLEILTAPDPRLRVQSKQVTDVASVQTLIDDLLDTLYATDNGIGLAAPQVGREEAIVVIDLSDNRDQPLVLINPKVVSGSNKEMGQEGCLSVPDYYADVERYTSVVVEALDREGKPLRIETSDFLAIVMQHEIDHLSGNLFIDYLSPLKQQMAMKKVKKHVKNRAR

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	ACTINONIN
formula_weight	385.5 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

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

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	213

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6. Citations (1)

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length_a	72.890 Å
length_b	72.890 Å
length_c	150.720 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 43 21 2
int_tables_number	96
crystal_system	tetragonal

resolution	1.820 Å
resolution_low	48.770 Å
r_factor	0.1823
r_work	0.1805
r_free	0.2197

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

Crystal structure of Def2 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