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9qbl

Crystal structure of Xanthobacter autotrophicus SPARDA mutant lacking DREN nuclease domains

Method: X-RAY DIFFRACTION D_max: 118.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qbl
deposition_date	2025-03-03
title	Crystal structure of Xanthobacter autotrophicus SPARDA mutant lacking DREN nuclease domains
keywords	Protein-nucleic acid interactions, Argonaute, pAgo, guide and target specificity, RNA BINDING PROTEIN; RNA BINDING PROTEIN
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	37.19 Å
rg_electron	36.30 Å
i0	433574000.00
molecular_weight	167900.0 kDa
excluded_volume	209910 Å³
envelope_volume	276040 Å³
shell_volume	62220 Å³
envelope_diameter	128.9 Å
shell_rg	43.63 Å
envelope_rg	35.40 Å
shape_rg	36.30 Å
total_rg	36.80 Å
total_atoms	11794
n_residues	1442
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	118.9 Å
rg_real	37.04 Å
rg_real_error	0.66 Å
i0_real	4.3360e+08
i0_real_error	6.4490e+06
rg_reciprocal	37.13 Å
i0_reciprocal	433600000.0000
total_estimate	0.8897
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	47.0 Å
skewness	0.239
kurtosis	-0.378
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0001
highest_alpha	62640000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.896

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4. Crystallography & Experiment

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5. Entities & Polymer Info (10)

Entity 1 polymer

description	DUF4365 domain-containing protein
formula_weight	37138.7 kDa
mutation	Deletion of N-terminal DUF4365 domain (1-153) and N-terminal His-tag
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C
atom_count	13446

MAGSHHHHHHGMASMTGGQQMGRSGWELQPGVFLPPLNKGEDAIINLLRIRLPDEIFISTSPFGSGRDAVPELVKHGNVRFDWVIRKRRFVSFFDPREYGTRAIVDLDQVEAVDTKLIAFNDEQDDLNDTMDLLRRTVERQTATQLSFLRKDRLFHFKAVGVGKSRSYRYMSNVNETSAKVVSAYSSKKKDGWGYVRHHAARLRFERLADEWFLVIDPDFHFTTDGFQPHRYPEALLAGKKRLERNAAVRGQVTMWQHLLVESGKHEVGLFDADKPAPLLQFERLPVIQLSQAVPESSWNRTDPRAKEMEAQDLFEEGGVG

Source

organism	Xanthobacter autotrophicus Py2
ncbi_taxonomy_id	78245
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Protein argonaute
formula_weight	53900.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,D

MTFKAHVFDEPMLEFGDGGQHCDPRQGLREHGPLQPRSGDVIRVGVIGTDDTVAGFTEFLAETGRGIESGNKQLINLNPDFPGLGNQNPFRCKFEVPDGATVTISRRQVNDITGIGRHDEAVRHAVELISSQLSALVEGSAKPDVIVLALPIPLIEKLVNAKSEGEDSDDDVDGGDMLNFRDLLKAKTLHLPVPTQIVWPDTWDDAAKIPRKIKRDSNRQTQVKATRAWNLLNALFYKAGKVPWRLLPDQAEYRTSFLGIGFYRDLDGQQLWTSTAQMFDERGRGLILRGARAQTETRGRHPYLTAKDAEDLVVQSIAAYKAHHRHVPARLVVLKTSRFRSEEAEGIDAALGKSGIEMSDLVWVQESSPIAIFRDGNYPVLRGTFVDLDGKGLLYTRGSVPFYGTFPGLRVPRPLLLVPHENSDSTILTLAKDVLALTKVNWNTTQFDQKLPAPIKAAREVGRILKHVEFGTAVSSDFRRYT

Source

organism	Xanthobacter autotrophicus Py2
ncbi_taxonomy_id	78245
host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

description	ACETIC ACID
formula_weight	60.1 kDa
src_method	syn
entity_count	5

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	7

Entity 5 non-polymer

description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	122.1 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	5

Entity 7 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	3

Entity 8 non-polymer

description	BETA-MERCAPTOETHANOL
formula_weight	78.1 kDa
src_method	syn
entity_count	5

Entity 9 non-polymer

description	D(-)-TARTARIC ACID
formula_weight	150.1 kDa
src_method	syn
entity_count	2

Entity 10 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1228

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6. Citations (1)

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length_a	72.706 Å
length_b	155.396 Å
length_c	161.338 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	—

resolution	1.500 Å
resolution_low	80.670 Å
r_factor	0.2000
r_work	0.1960
r_free	0.2370

fit	/app/data/saxs_computation/qb/9qbl/9qbl.fit
pddf	/app/data/pr_computation/qb/9qbl/9qbl.pr.out
profile	/app/data/saxs_computation/qb/9qbl/9qbl.dat

Crystal structure of Xanthobacter autotrophicus SPARDA mutant lacking DREN nuclease domains

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

5. Entities & Polymer Info (10)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)