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9r0y

Crystal structure of NDM-1 with thiol compound 22b

Method: X-RAY DIFFRACTION D_max: 81.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r0y
deposition_date	2025-04-24
last_revision	2025-07-09
title	Crystal structure of NDM-1 with thiol compound 22b
keywords	inhibitor, thiol, antimicrobial resistance, metall-beta-lactamase, 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	24.08 Å
rg_electron	23.50 Å
i0	43668100.00
molecular_weight	49183.0 kDa
excluded_volume	60511 Å³
envelope_volume	70399 Å³
shell_volume	25359 Å³
envelope_diameter	84.6 Å
shell_rg	30.34 Å
envelope_rg	23.85 Å
shape_rg	23.58 Å
total_rg	24.04 Å
total_atoms	6696
n_residues	459
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	81.8 Å
rg_real	24.17 Å
rg_real_error	0.60 Å
i0_real	4.3670e+07
i0_real_error	6.2440e+05
rg_reciprocal	24.15 Å
i0_reciprocal	43670000.0000
total_estimate	0.8569
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.6 Å
skewness	0.495
kurtosis	-0.185
angular_range	— – 0.3300 Å⁻¹
current_alpha	0.0000
highest_alpha	17020000.0000
n_real_points	65
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.754; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.937; Smooth: 0.937

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

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	7320

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	1

Entity 4 non-polymer

description	~{N}-naphthalen-2-yl-2-sulfanyl-ethanamide
formula_weight	217.3 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	472

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6. Citations (1)

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length_a	68.383 Å
length_b	73.350 Å
length_c	76.955 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	1.270 Å
resolution_low	50.020 Å
r_factor	0.1660
r_work	0.1655
r_free	0.1912

fit	/app/data/saxs_computation/r0/9r0y/9r0y.fit
pddf	/app/data/pr_computation/r0/9r0y/9r0y.pr.out
profile	/app/data/saxs_computation/r0/9r0y/9r0y.dat