← Back to search

9q3k

;Structure of LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme with a single catalytic histidine residue from Streptococcus plurextorum ;

Method: ELECTRON MICROSCOPY D_max: 135.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9q3k
deposition_date	2025-08-18
last_revision	2025-09-24
title	;Structure of LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme with a single catalytic histidine residue from Streptococcus plurextorum ;
keywords	Racemase and epimerase activity, acting on hydroxy acids and derivatives, metal ion binding, catalytic activity, ISOMERASE; ISOMERASE
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	45.57 Å
rg_electron	44.86 Å
i0	2663090000.00
molecular_weight	431690.0 kDa
excluded_volume	539350 Å³
envelope_volume	638190 Å³
shell_volume	109760 Å³
envelope_diameter	139.0 Å
shell_rg	55.70 Å
envelope_rg	44.20 Å
shape_rg	44.82 Å
total_rg	45.32 Å
total_atoms	30317
n_residues	3840
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

▼

3. P(r) Analysis (GNOM)

dmax	135.6 Å
rg_real	45.15 Å
rg_real_error	0.81 Å
i0_real	2.6630e+09
i0_real_error	4.0290e+07
rg_reciprocal	45.57 Å
i0_reciprocal	2664000000.0000
total_estimate	0.8883
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	62.0 Å
skewness	-0.018
kurtosis	-0.518
angular_range	— – 0.1750 Å⁻¹
current_alpha	0.0000
highest_alpha	386700000.0000
n_real_points	36
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.947; Smooth: 0.878

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

Entity 1 polymer

description	LarA-like nickel-pincer nucleotide cofactor-utilizing enzyme
formula_weight	56339.3 kDa
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	B,D,A,H,E,F,C,G
atom_count	30332

MKIDFEYGHGTMTADLPDTTDIFIPGETVADPECLPEDQIEAATLDSIRNPLGMPPLTELAKPGSKVTIVFPDRVKGGEQATAHRKVSIKLILQELYSVGVKKEDILLICSNGLHRKNTEKEILGVLGPDLYHQFAPTGQIINHDSEDYEHLVDLGKTKQGDPVIMNKYVYESDVAILIGHTQGNPYGGYSGGYKHCSTGITHWKSIASHHVPKVMHRKDFVPVNNNSLMRHKFDEIGMHMEEKMGKKFFCCDAVLDTKSRQIEINSGAADEVQKKAWKLGNARTYVPFAEKKYDIIVFGMPQFFHYGDGMGTNPIMLMQALSAQVIRHKRIMSDNCVFICASTCNGYFNESLWPYLPELYDLFQKEGNTLVDLNQYGEYFATNEEYIRKYRYAHAFHPFHGFSMISCAHLAEKHTAAIYLVGAEKPGYARGMGLKTRATFEEALEDAKKKFVGQEPNILALPKAFKTAAVHLMMKNDLPPMTPRYEENHWSHPQFEK

Source

organism	Streptococcus plurextorum
ncbi_taxonomy_id	456876
host_organism	Lactococcus lactis

Entity 2 non-polymer

description	NICKEL (II) ION
formula_weight	58.7 kDa
src_method	syn
entity_count	8

Entity 3 non-polymer

description	3-methanethioyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-5-(sulfanylcarbonyl)pyridin-1-ium
formula_weight	396.4 kDa
src_method	syn
entity_count	8

▶

6. Citations (1)

▶

length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.20 Å
resolution_method	—
num_particles	571000

fit	/app/data/saxs_computation/q3/9q3k/9q3k.fit
pddf	/app/data/pr_computation/q3/9q3k/9q3k.pr.out
profile	/app/data/saxs_computation/q3/9q3k/9q3k.dat