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9q1a

Open state of lysine 5,6-aminomutase from Thermoanaerobacter tengcongensis

Method: ELECTRON MICROSCOPY D_max: 136.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9q1a
deposition_date	2025-08-13
title	Open state of lysine 5,6-aminomutase from Thermoanaerobacter tengcongensis
keywords	lysine 5, 6-aminomutase, cobalamin, vitamin B12, pyridoxal phosphate, radical, ISOMERASE; ISOMERASE
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	39.64 Å
rg_electron	39.70 Å
i0	444081000.00
molecular_weight	175840.0 kDa
excluded_volume	221690 Å³
envelope_volume	274090 Å³
shell_volume	58512 Å³
envelope_diameter	147.0 Å
shell_rg	44.28 Å
envelope_rg	39.56 Å
shape_rg	39.69 Å
total_rg	39.97 Å
total_atoms	24813
n_residues	1545
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	136.6 Å
rg_real	39.86 Å
rg_real_error	1.29 Å
i0_real	4.4410e+08
i0_real_error	7.5310e+06
rg_reciprocal	39.73 Å
i0_reciprocal	444000000.0000
total_estimate	0.8588
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	44.4 Å
skewness	0.494
kurtosis	-0.239
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	72960000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.766; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.953; Smooth: 0.908

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	D-lysine 5,6-aminomutase beta subunit
formula_weight	28612.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	24813

QYDTTLDLTRVKPYGDTMNDGKVQLSFTLPVPDGAKAVEAAKQLAKKMGLENPMVVYHAPLDKNFTFFIIYGSLIHTVDYTSIQVQELEIKAMSMEETNEYIKKHIGRKVVVVGATTGTDAHTVGLDAIMNMKGYAGHYGLERYEMIEAYNLGSQVPNEEFVKKAIEVGADALLVSQTVTQKDAHIKNLTHLVELLEAEGIRDKVLLICGGPRITHELAKELGYDAGFGPGTFADHVATFIVTEMVKRKIPGLKGYK

Source

organism	Caldanaerobacter subterraneus subsp. tengcongensis
ncbi_taxonomy_id	119072
host_organism	Escherichia coli

Entity 2 polymer

description	D-lysine 5,6-aminomutase alpha subunit
formula_weight	57943.5 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,D

RESKLNLDWELVDKAREAARNIVKDTQKFIDAHTTVSVERTVCRLLGIDGVNDLGVPLPNVVVDHIKSKGNLSLGAATYIGNAMIYTGLSPQEIAERVAKGELDLTSIPMADLFEIKLAVQDIAIKTVEKIRENRRKREEFLKKYGDKEGPLLYVIVATGNIYEDVVQAQAAARQGADVIAVIRATAQSLLDYVPYGPTTEGFGGTYATQENFRIMRKALDEVSEELGRYIRLCNYASGLCMPEIAAMGALERLDVMLNDALYGILFRDINMKRTMVDQFFSRVINGFAGIIINTGEDNYLTTADAYEKAHTVLASQLINEQFALIAGIPEEQMGLGHAFEMNPDLRNGFLYELAQAQMVREIFPKAPLKYMPPTKYMTGNIFKGHVQDAMFNVVTIMTKQRIHLLGMLTEAIHTPFMSDRALSIESAKYIFNNMADIADEIYFKEGGIIQRRANEVLKKAYELLKEIEQEGLFKALEQGKFADIKRPIDGGKGLEGVVEKDPNYFNPFIDLMLRGD

Source

organism	Caldanaerobacter subterraneus subsp. tengcongensis
ncbi_taxonomy_id	119072
host_organism	Escherichia coli

Entity 3 non-polymer

description	COBALAMIN
formula_weight	1330.4 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	5'-DEOXYADENOSINE
formula_weight	251.2 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	2.83 Å
resolution_method	—
num_particles	1482472

fit	/app/data/saxs_computation/q1/9q1a/9q1a.fit
pddf	/app/data/pr_computation/q1/9q1a/9q1a.pr.out
profile	/app/data/saxs_computation/q1/9q1a/9q1a.dat

Open state of lysine 5,6-aminomutase from Thermoanaerobacter tengcongensis

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

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)