← Back to search

9r0x

Crystal structure of NDM-1 with thiol compound 14a

Method: X-RAY DIFFRACTION D_max: 81.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9r0x
deposition_date	2025-04-24
last_revision	2025-07-09
title	Crystal structure of NDM-1 with thiol compound 14a
keywords	inhibitor, thiol, antimicrobial resistance, metall-beta-lactamase, ANTIMICROBIAL PROTEIN; ANTIMICROBIAL PROTEIN
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	24.04 Å
rg_electron	23.42 Å
i0	43305000.00
molecular_weight	49176.0 kDa
excluded_volume	60709 Å³
envelope_volume	69903 Å³
shell_volume	25290 Å³
envelope_diameter	82.8 Å
shell_rg	30.25 Å
envelope_rg	23.70 Å
shape_rg	23.49 Å
total_rg	23.98 Å
total_atoms	6756
n_residues	458
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

▼

3. P(r) Analysis (GNOM)

dmax	81.7 Å
rg_real	24.12 Å
rg_real_error	0.63 Å
i0_real	4.3300e+07
i0_real_error	6.0210e+05
rg_reciprocal	24.10 Å
i0_reciprocal	43300000.0000
total_estimate	0.8536
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.5 Å
skewness	0.485
kurtosis	-0.213
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	16850000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.757; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.935; Smooth: 0.888

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (6)

Entity 1 polymer

description	Metallo-beta-lactamase type 2
formula_weight	26045.3 kDa
ec_number	3.5.2.6
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7772

GSHMGEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR

Source

organism	Klebsiella pneumoniae
ncbi_taxonomy_id	573
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	~{N}-(3-chlorophenyl)-2-sulfanyl-ethanamide
formula_weight	201.7 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	560

▶

6. Citations (1)

▶

length_a	68.280 Å
length_b	73.448 Å
length_c	76.901 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	1.130 Å
resolution_low	51.060 Å
r_factor	0.1201
r_work	0.1187
r_free	0.1460

fit	/app/data/saxs_computation/r0/9r0x/9r0x.fit
pddf	/app/data/pr_computation/r0/9r0x/9r0x.pr.out
profile	/app/data/saxs_computation/r0/9r0x/9r0x.dat