SAXSdb — 9x4g

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1. Structure Basics

entry_id	9x4g
deposition_date	2025-10-10
title	Structure Of the KEOPS dimer
keywords	;tRNA modification, t6A, KEOPS-tRNA complex, cryo-EM structure, substrate recognition, catalytic mechanism, regulation principle, TRANSFERASE ;; TRANSFERASE
method	ELECTRON MICROSCOPY

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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	49.88 Å
rg_electron	50.90 Å
i0	402877000.00
molecular_weight	167740.0 kDa
excluded_volume	211130 Å³
envelope_volume	309120 Å³
shell_volume	52896 Å³
envelope_diameter	175.1 Å
shell_rg	50.61 Å
envelope_rg	50.68 Å
shape_rg	50.92 Å
total_rg	50.85 Å
total_atoms	11768
n_residues	1518
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	162.3 Å
rg_real	50.48 Å
rg_real_error	1.90 Å
i0_real	4.0290e+08
i0_real_error	8.5510e+06
rg_reciprocal	49.89 Å
i0_reciprocal	402600000.0000
total_estimate	0.8067
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	50.7 Å
skewness	0.445
kurtosis	-0.507
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	19230000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.876; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.802; Smooth: 0.054

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	N(6)-L-threonylcarbamoyladenine synthase
formula_weight	36859.7 kDa
ec_number	2.3.1.234
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,E
atom_count	11768

MVCVIGIEGSANKIGVGIIRDGVVLSNPRATFHAPPGEGFRPTETAQHHRQQIVRLVGEAIKLANIQNPELEIDGIAYTKGPGMGAPLQVGAIVARTLSLTWKKPIIPVNHCVGHIEMGRLITGADNPVVLYVSGGNTQVISYTKKRYRIFGETIDIAVGNCLDRFARVLKLPNAPSPGYNIEQLAKNGKKLMELPYSVKGMDVSLSGILSLIEKKAPKLIESGDFTPEDLCFSLQETVFAMLIEITERAMAHTSSKELLIVGGVGCNLRLQEMASAMCAERGAHLFATDERFCIDNGAMIARAGELMLASGMRFDLRKTTTTQRYRTDQVHVEWRD

Source

organism	Caenorhabditis elegans
ncbi_taxonomy_id	6239
host_organism	Escherichia coli

Entity 2 polymer

description	non-specific serine/threonine protein kinase
formula_weight	27544.5 kDa
ec_number	2.7.11.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,F

MTAATTSSDSEGEMDFETTIETGFGYQIDGLLYQGAEAKVTKCIWLGRQAIIKERFSKGYRHPTLDTQLNKARTKQEIRGLNKARELGIHVPAVYFIDNEKNQLIMEFVPGSTAKNWISQLNPADFDAKTREFGQIFGEKLGKLHRGGLIHGDLTTSNIILRDDDLQKMTFIDFGLSSQGKVTPEEKGVDLYVLERAVISTHDKCAALIEGLMEGYKKADGKQFVAVEKKLNEIRLRGRKRDMIG

Source

organism	Caenorhabditis elegans
ncbi_taxonomy_id	6239
host_organism	Escherichia coli

Entity 3 polymer

description	EKC/KEOPS complex subunit TPRKB
formula_weight	20215.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,G

MKHSHLYELQPDPYDFTQRKTCRVCLFKDVKNAAELSQQLKEGKIDAALIRAELVLEPFVLLAAANRAVHQSAHNRMSCRSLAAELVYSLSPSRNITDSLVTFGIAEHSTAIIAAIFDDDSGKAMKKLAKAIKGTPVPLMEGLPKFANVNMIKKVYQVGNPAFVEEGLSDHIVSRMVSKDFVS

Source

organism	Caenorhabditis elegans
ncbi_taxonomy_id	6239
host_organism	Escherichia coli

Entity 4 polymer

description	L antigen family member 3
formula_weight	13223.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	D,H

MEVDTSSSSSSEDECDPSSPSTAYIHSASVRLSVGTEEAARTVADVIKIDKEPRRSGARREVCSEGEFVVIKIESKDPKSLSKSIANAVDMIDLSVKTIKLCENLGKSKENGLKRKLSNGSQA

Source

organism	Caenorhabditis elegans
ncbi_taxonomy_id	6239
host_organism	Escherichia coli

Entity 5 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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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	3.100 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.10 Å
resolution_method	—
num_particles	241539

fit	/app/data/saxs_computation/x4/9x4g/9x4g.fit
pddf	/app/data/pr_computation/x4/9x4g/9x4g.pr.out
profile	/app/data/saxs_computation/x4/9x4g/9x4g.dat

Structure Of the KEOPS dimer

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

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)