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9ra3

Crystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with alkene C1

Method: X-RAY DIFFRACTION D_max: 128.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ra3
deposition_date	2025-05-20
last_revision	2026-06-03
title	Crystal structure of the transpeptidase LdtMt2 from Mycobacterium tuberculosis in complex with alkene C1
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	35.18 Å
rg_electron	35.34 Å
i0	173041000.00
molecular_weight	68967.0 kDa
excluded_volume	65848 Å³
envelope_volume	124610 Å³
shell_volume	32763 Å³
envelope_diameter	129.8 Å
shell_rg	37.16 Å
envelope_rg	35.42 Å
shape_rg	35.29 Å
total_rg	35.53 Å
total_atoms	5206
n_residues	702
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	128.8 Å
rg_real	35.58 Å
rg_real_error	1.61 Å
i0_real	1.7300e+08
i0_real_error	2.9570e+06
rg_reciprocal	35.33 Å
i0_reciprocal	173000000.0000
total_estimate	0.8117
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	37.2 Å
skewness	0.630
kurtosis	0.033
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0000
highest_alpha	5486000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.679; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.686; Smooth: 0.825

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

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

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5448

QSDLLVPKLTASVTDGAVGVTVDAPVSVTAADGVLAAVTMVNDNGRPVAGRLSPDGLRWSTTEQLGYNRRYTLNATALGLGGAATRQLTFQTSSPAHLTMPYVMPGDGEVVGVGEPVAIRFDENIADRGAAEKAIKITTNPPVEGAFYWLNNREVRWRPEHFWKPGTAVDVAVNTYGVDLGEGMFGEDNVQTHFTIGDEVIATADDNTKILTVRVNGEVVKSMPTSMGKDSTPTANGIYIVGSRYKHIIMDSSTYGVPVNSPNGYRTDVDWATQISYSGVFVHSAPWSVGAQGHTNTSHGCLNVSPSNAQWFYDHVKRGDIVEVVNTVGGTLPGIDGLGDWNIPWDQWRAGNAKA

Source

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

Entity 2 non-polymer

description	1-ethylisoquinoline
formula_weight	157.2 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	5

Entity 6 non-polymer

description	NITRATE ION
formula_weight	62.0 kDa
src_method	syn
entity_count	9

Entity 7 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	nat
entity_count	2

Entity 8 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 9 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	224

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6. Citations (1)

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length_a	61.390 Å
length_b	93.930 Å
length_c	75.250 Å
angle_alpha	90.00 °
angle_beta	92.68 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.300 Å
resolution_low	46.970 Å
r_factor	0.2422
r_work	0.2406
r_free	0.2717

fit	/app/data/saxs_computation/ra/9ra3/9ra3.fit
pddf	/app/data/pr_computation/ra/9ra3/9ra3.pr.out
profile	/app/data/saxs_computation/ra/9ra3/9ra3.dat