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9ri2

Crystal structure of bacillithiol methyltransferase NmbA from Chlorobaculum tepidum

Method: X-RAY DIFFRACTION D_max: 81.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ri2
deposition_date	2025-06-10
title	Crystal structure of bacillithiol methyltransferase NmbA from Chlorobaculum tepidum
keywords	natural product methyl transferase, low-molecular weight thiol, bacillithiol, SAM, TRANSFERASE; TRANSFERASE
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	24.74 Å
rg_electron	23.88 Å
i0	47416000.00
molecular_weight	52757.0 kDa
excluded_volume	65760 Å³
envelope_volume	79420 Å³
shell_volume	27725 Å³
envelope_diameter	80.4 Å
shell_rg	30.97 Å
envelope_rg	23.95 Å
shape_rg	23.88 Å
total_rg	24.68 Å
total_atoms	3727
n_residues	455
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	81.1 Å
rg_real	24.72 Å
rg_real_error	0.57 Å
i0_real	4.7420e+07
i0_real_error	6.9140e+05
rg_reciprocal	24.72 Å
i0_reciprocal	47420000.0000
total_estimate	0.7987
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	27.1 Å
skewness	0.356
kurtosis	-0.396
angular_range	— – 0.3200 Å⁻¹
current_alpha	0.0000
highest_alpha	23580000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.815; Stabil: 0.982; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Methyltransferase, putative
formula_weight	30515.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3741

MSDHQSHSRGKNAREWFEEWFDHPLYLKVYHHRDAEEAERCVRTILDLTGIDPAWQPPHSVLDIACGAGRHALSFARTGLRVTANDLSPYLLDQARKQAKAEGINMEFSRQDMRTIRFERRFDLIAQLFSSFGYFETDQEDRDVIANIASLLNPGGWYVLDLINPVQLKSQFTPRTERNSESLSIIEERTLSERHVTKKITLHEANGRKHSFTESVRIYSPAEAFSLLESGGFAVERVVGDYEGSPFDEATSPRMMLLARLLVSRS

Source

organism	Chlorobaculum tepidum TLS
ncbi_taxonomy_id	194439
host_organism	Escherichia coli

Entity 2 non-polymer

description	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	282.3 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	CITRATE ANION
formula_weight	189.1 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	14

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6. Citations (1)

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length_a	53.751 Å
length_b	55.517 Å
length_c	186.017 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	orthorhombic

resolution	2.700 Å
resolution_low	47.670 Å
r_factor	0.2147
r_work	0.2127
r_free	0.2529

fit	/app/data/saxs_computation/ri/9ri2/9ri2.fit
pddf	/app/data/pr_computation/ri/9ri2/9ri2.pr.out
profile	/app/data/saxs_computation/ri/9ri2/9ri2.dat

Crystal structure of bacillithiol methyltransferase NmbA from Chlorobaculum tepidum

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