SAXSdb — 9v4o

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1. Structure Basics

entry_id	9v4o
deposition_date	2025-05-24
last_revision	2025-11-26
title	Cryo-EM structure of A. thaliana MET1 with bound SAH
keywords	DNA methylation, covalent AtMET1-DNA complex, Cryo-EM structure, epigenetic regulation, GENE REGULATION; GENE REGULATION
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	37.68 Å
rg_electron	37.33 Å
i0	219364000.00
molecular_weight	120720.0 kDa
excluded_volume	151500 Å³
envelope_volume	212040 Å³
shell_volume	47961 Å³
envelope_diameter	126.2 Å
shell_rg	42.97 Å
envelope_rg	36.91 Å
shape_rg	37.29 Å
total_rg	37.84 Å
total_atoms	8498
n_residues	1064
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	124.7 Å
rg_real	37.67 Å
rg_real_error	0.85 Å
i0_real	2.1940e+08
i0_real_error	3.4090e+06
rg_reciprocal	37.68 Å
i0_reciprocal	219400000.0000
total_estimate	0.6823
solution_quality	REASONABLE a REASONABLE solution
n_peaks	0
r_peak_primary	— Å
skewness	0.256
kurtosis	-0.544
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	49220000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 0.080; Positv: 1.000; Valcen: 0.992; Smooth: 0.891

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	DNA (cytosine-5)-methyltransferase 1
formula_weight	177588.1 kDa
ec_number	2.1.1.37
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	8498

MSYYHHHHHHHHHHDYDIDYKDDDDKPTTENLYFQGAMGSMVENGAKAAKRKKRPLPEIQEVEDVPRTRRPRRAAACTSFKEKSIRVCEKSATIEVKKQQIVEEEFLALRLTALETDVEDRPTRRLNDFVLFDSDGVPQPLEMLEIHDIFVSGAILPSDVCTDKEKEKGVRCTSFGRVEHWSISGYEDGSPVIWISTELADYDCRKPAASYRKVYDYFYEKARASVAVYKKLSKSSGGDPDIGLEELLAAVVRSMSSGSKYFSSGAAIIDFVISQGDFIYNQLAGLDETAKKHESSYVEIPVLVALREKSSKIDKPLQRERNPSNGVRIKEVSQVAESEALTSDQLVDGTDDDRRYAILLQDEENRKSMQQPRKNSSSGSASNMFYIKINEDEIANDYPLPSYYKTSEEETDELILYDASYEVQSEHLPHRMLHNWALYNSDLRFISLELLPMKQCDDIDVNIFGSGVVTDDNGSWISLNDPDSGSQSHDPDGMCIFLSQIKEWMIEFGSDDIISISIRTDVAWYRLGKPSKLYAPWWKPVLKTARVGISILTFLRVESRVARLSFADVTKRLSGLQANDKAYISSDPLAVERYLVVHGQIILQLFAVYPDDNVKRCPFVVGLASKLEDRHHTKWIIKKKKISLKELNLNPRAGMAPVASKRKAMQATTTRLVNRIWGEFYSNYSPEDPLQATAAENGEDEVEEEGGNGEEEVEEEGENGLTEDTVPEPVEVQKPHTPKKIRGSSGKREIKWDGESLGKTSAGEPLYQQALVGGEMVAVGGAVTLEVDDPDEMPAIYFVEYMFESTDHCKMLHGRFLQRGSMTVLGNAANERELFLTNECMTTQLKDIKGVASFEIRSRPWGHQYRKKNITADKLDWARALERKVKDLPTEYYCKSLYSPERGGFFSLPLSDIGRSSGFCTSCKIREDEEKRSTIKLNVSKTGFFINGIEYSVEDFVYVNPDSIGGLKEGSKTSFKSGRNIGLRAYVVCQLLEIVPKESRKADLGSFDVKVRRFYRPEDVSAEKAYASDIQELYFSQDTVVLPPGALEGKCEVRKKSDMPLSREYPISDHIFFCDLFFDTSKGSLKQLPANMKPKFSTIKDDTLLRKKKGKGVESEIESEIVKPVEPPKEIRLATLDIFAGCGGLSHGLKKAGVSDAKWAIEYEEPAGQAFKQNHPESTVFVDNCNVILRAIMEKGGDQDDCVSTTEANELAAKLTEEQKSTLPLPGQVDFINGGPPCQGFSGMNRFNQSSWSKVQCEMILAFLSFADYFRPRYFLLENVRTFVSFNKGQTFQLTLASLLEMGYQVRFGILEAGAYGVSQSRKRAFIWAAAPEEVLPEWPEPMHVFGVPKLKISLSQGLHYAAVRSTALGAPFRPITVRDTIGDLPSVENGDSRTNKEYKEVAVSWFQKEIRGNTIALTDHICKAMNELNLIRCKLIPTRPGADWHDLPKRKVTLSDGRVEEMIPFCLPNTAERHNGWKGLYGRLDWQGNFPTSVTDPQPMGKVGMCFHPEQHRILTVRECARSQGFPDSYEFAGNINHKHRQIGNAVPPPLAFALGRKLKEALHLKKSPQHQP

Source

organism	Arabidopsis thaliana
common_name	thale cress
ncbi_taxonomy_id	3702
host_organism	Baculovirus expression vector pFastBac1-HM

Entity 2 non-polymer

description	S-ADENOSYL-L-HOMOCYSTEINE
formula_weight	384.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	1

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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	2.92 Å
resolution_method	—
num_particles	629218

fit	/app/data/saxs_computation/v4/9v4o/9v4o.fit
pddf	/app/data/pr_computation/v4/9v4o/9v4o.pr.out
profile	/app/data/saxs_computation/v4/9v4o/9v4o.dat

Cryo-EM structure of A. thaliana MET1 with bound SAH

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

EM 3D