SAXSdb — 9r3w

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1. Structure Basics

entry_id	9r3w
deposition_date	2025-05-06
title	Fungal tRNA ligase Trl1-LIG-KIN
keywords	tRNA ligase, polynucleotide kinase, tRNA splicing, adenylyltransferase, LIGASE; LIGASE
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	28.44 Å
rg_electron	27.52 Å
i0	83287300.00
molecular_weight	70022.0 kDa
excluded_volume	86975 Å³
envelope_volume	108950 Å³
shell_volume	32921 Å³
envelope_diameter	93.0 Å
shell_rg	35.05 Å
envelope_rg	27.08 Å
shape_rg	27.49 Å
total_rg	28.33 Å
total_atoms	4929
n_residues	610
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	88.2 Å
rg_real	28.35 Å
rg_real_error	0.58 Å
i0_real	8.3290e+07
i0_real_error	1.0860e+06
rg_reciprocal	28.38 Å
i0_reciprocal	83290000.0000
total_estimate	0.9060
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	33.1 Å
skewness	0.219
kurtosis	-0.537
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	21550000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.895

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	tRNA ligase
formula_weight	70812.0 kDa
ec_number	6.5.1.3
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5277

GSHMDGTAEKQRDSLASRYKASTDYAKDAEGLTAPYVSQDPQETAALVRALDDAAKKGKKSGGFSVKKTRYAVASSPTGAEVDSWRFNDWDYKKPDLPTYARGLFTTRTQHGVPEIAVRGYDKFFNIDETRDTAWSAIRERTKGPYELTLKENGCIIFISGLEDGTLLVCSKHSTGDRSDVALSHSSAGEKHLEAQLERIGKTKEELARELRKRNATAVAELCDDSFEEHILAYGPDKAGLYLHGINLNIPEFITYPSPLVQKFAEDWGFRKTGLIIIDNIDDVKAFLEEVAETGAHDGRDVEGFVIRCKKSTNPGVGPYHDWFFKYKFEEPYLMYRQWRECTKALISGKQPKIKKHVKITEEYLLYARKRLAADPKLAKLYNQNHGIIKLRNDFLEYKNMKGTDAANLEDDGAASVTRDIILVPIATIGCGKTTLGVALTKLFGWGHIQNDNITGSKRPPRFTKAVLDELNEHPAVFADRNNSMRQERKQLLTDVKMQHTTARLVALHFVHDDINTVRKVTQERVIQRGDNHQTIQAATDVNKVIGIMEGFIHRFEPCDPEKDPDEGFDAVIDLDPTAGSRENLEVVIRELHRLYPNFVKEVPPAEAMDEAIKFAMESYKPDLRHI

Source

organism	Thermochaetoides thermophila
ncbi_taxonomy_id	209285
host_organism	Escherichia coli

Entity 2 non-polymer

description	GUANOSINE-5'-DIPHOSPHATE
formula_weight	443.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
formula_weight	505.2 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	348

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6. Citations (1)

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length_a	112.674 Å
length_b	112.674 Å
length_c	108.270 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 4 21 2
int_tables_number	90
crystal_system	tetragonal

resolution	1.890 Å
resolution_low	48.800 Å
r_factor	0.1835
r_work	0.1816
r_free	0.2187

fit	/app/data/saxs_computation/r3/9r3w/9r3w.fit
pddf	/app/data/pr_computation/r3/9r3w/9r3w.pr.out
profile	/app/data/saxs_computation/r3/9r3w/9r3w.dat

Fungal tRNA ligase Trl1-LIG-KIN

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