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9qlk

Structure of piperazate synthase from Streptomyces sp.

Method: X-RAY DIFFRACTION D_max: 128.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qlk
deposition_date	2025-03-21
title	Structure of piperazate synthase from Streptomyces sp.
keywords	Piperazate synthase, piperazic acid, N-N bond formation, heme-binding, LYASE; LYASE
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	41.18 Å
rg_electron	40.83 Å
i0	320412000.00
molecular_weight	145370.0 kDa
excluded_volume	181170 Å³
envelope_volume	236530 Å³
shell_volume	48318 Å³
envelope_diameter	133.6 Å
shell_rg	46.28 Å
envelope_rg	39.86 Å
shape_rg	40.81 Å
total_rg	41.18 Å
total_atoms	20184
n_residues	1274
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	128.7 Å
rg_real	41.11 Å
rg_real_error	1.20 Å
i0_real	3.2040e+08
i0_real_error	5.6740e+06
rg_reciprocal	41.18 Å
i0_reciprocal	320400000.0000
total_estimate	0.8843
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	64.3 Å
skewness	0.121
kurtosis	-0.790
angular_range	— – 0.1900 Å⁻¹
current_alpha	0.0000
highest_alpha	79390000.0000
n_real_points	39
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.757

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	FMN-binding negative transcriptional regulator
formula_weight	25619.8 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F
atom_count	20648

MAMYVPAVYQAREGRQLVEVVSQYPLAVLMTNGPSTPFSTHLPVIPASETDVDELVGSTLLGHMNRANPHWSALRAGIAAKAVFWGPNSYVTPMLYPSDPAAPTWNFVSVHVEGVLQPVHDDEETLAVVRRTAARLEGRFGAGWDQEGSLDYFRKILPGVGAFRLEVRSAQGMFKLSQDKEPAVRRRIREHFEADGTGPTRELGRAMRNFDEATEREYGALEHHHHHHH

Source

organism	Streptomyces sp. B93
ncbi_taxonomy_id	2824875
host_organism	Escherichia coli

Entity 2 non-polymer

description	PROTOPORPHYRIN IX CONTAINING FE
formula_weight	616.5 kDa
src_method	syn
entity_count	6

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	5

Entity 4 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

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

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	338

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6. Citations (1)

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length_a	141.708 Å
length_b	141.708 Å
length_c	57.128 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	18

space_group	P 32
int_tables_number	145
crystal_system	trigonal

resolution	2.140 Å
resolution_low	51.790 Å
r_factor	0.1962
r_work	0.1926
r_free	0.2652

fit	/app/data/saxs_computation/ql/9qlk/9qlk.fit
pddf	/app/data/pr_computation/ql/9qlk/9qlk.pr.out
profile	/app/data/saxs_computation/ql/9qlk/9qlk.dat