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9u9c

Crystal structure of NDM-1 in complex with hydrolyzed amoxicillin

Method: X-RAY DIFFRACTION D_max: 80.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u9c
deposition_date	2025-03-27
title	Crystal structure of NDM-1 in complex with hydrolyzed amoxicillin
keywords	Hydrolase, NDM-1; HYDROLASE
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	24.61 Å
rg_electron	24.21 Å
i0	87888200.00
molecular_weight	48371.0 kDa
excluded_volume	46297 Å³
envelope_volume	74142 Å³
shell_volume	26028 Å³
envelope_diameter	82.3 Å
shell_rg	31.07 Å
envelope_rg	24.29 Å
shape_rg	24.21 Å
total_rg	24.76 Å
total_atoms	3671
n_residues	480
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	80.6 Å
rg_real	24.68 Å
rg_real_error	0.52 Å
i0_real	8.7890e+07
i0_real_error	1.3330e+06
rg_reciprocal	24.66 Å
i0_reciprocal	87890000.0000
total_estimate	0.8788
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.6 Å
skewness	0.424
kurtosis	-0.387
angular_range	— – 0.3250 Å⁻¹
current_alpha	0.0000
highest_alpha	25720000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.938; Smooth: 0.958

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Metallo-beta-lactamase type 2
formula_weight	25631.8 kDa
ec_number	3.5.2.6
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4361

GEIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR

Source

organism	Klebsiella pneumoniae
ncbi_taxonomy_id	573
host_organism	Escherichia coli

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	5

Entity 3 non-polymer

description	;(2~{R},4~{S})-2-[(1~{R})-1-[[(2~{R})-2-azanyl-2-(4-hydroxyphenyl)ethanoyl]amino]-2-oxidanyl-2-oxidanylidene-ethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid ;
formula_weight	383.4 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	643

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6. Citations (1)

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length_a	39.210 Å
length_b	79.330 Å
length_c	134.480 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	1.250 Å
resolution_low	39.030 Å
r_factor	0.1518
r_work	0.1508
r_free	0.1696

fit	/app/data/saxs_computation/u9/9u9c/9u9c.fit
pddf	/app/data/pr_computation/u9/9u9c/9u9c.pr.out
profile	/app/data/saxs_computation/u9/9u9c/9u9c.dat

Crystal structure of NDM-1 in complex with hydrolyzed amoxicillin

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