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9ra4

Crystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with cyclobutene C2

Method: X-RAY DIFFRACTION D_max: 95.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ra4
deposition_date	2025-05-20
last_revision	2026-06-03
title	Crystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with cyclobutene C2
keywords	L, D-transpeptidase 2, LdtMt2, mycobacterium tuberculosis, covalent inhibitor, ANTIMICROBIAL PROTEIN; ANTIMICROBIAL PROTEIN
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	26.96 Å
rg_electron	26.85 Å
i0	46610800.00
molecular_weight	34975.0 kDa
excluded_volume	33487 Å³
envelope_volume	59162 Å³
shell_volume	20649 Å³
envelope_diameter	98.5 Å
shell_rg	30.81 Å
envelope_rg	27.24 Å
shape_rg	26.83 Å
total_rg	27.21 Å
total_atoms	2644
n_residues	350
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	95.0 Å
rg_real	27.37 Å
rg_real_error	0.94 Å
i0_real	4.6610e+07
i0_real_error	6.8270e+05
rg_reciprocal	27.24 Å
i0_reciprocal	46610000.0000
total_estimate	0.7880
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.5 Å
skewness	0.614
kurtosis	-0.259
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	5222000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.640; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.386; Smooth: 0.933

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	L,D-transpeptidase 2
formula_weight	38009.1 kDa
ec_number	2.3.2.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2840

QSDLLVPKLTASVTDGAVGVTVDAPVSVTAADGVLAAVTMVNDNGRPVAGRLSPDGLRWSTTEQLGYNRRYTLNATALGLGGAATRQLTFQTSSPAHLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSSTYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNAKA

Source

organism	Mycobacterium tuberculosis
ncbi_taxonomy_id	1773
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	1-cyclobutylisoquinoline
formula_weight	183.2 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	NITRATE ION
formula_weight	62.0 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	nat
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	187

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6. Citations (1)

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length_a	76.055 Å
length_b	94.608 Å
length_c	60.248 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 2
int_tables_number	18
crystal_system	—

resolution	2.250 Å
resolution_low	60.250 Å
r_factor	0.2329
r_work	0.2315
r_free	0.2598

fit	/app/data/saxs_computation/ra/9ra4/9ra4.fit
pddf	/app/data/pr_computation/ra/9ra4/9ra4.pr.out
profile	/app/data/saxs_computation/ra/9ra4/9ra4.dat