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9rfm

Crystal structure of the metallo-beta-lactamase VIM-1 with 1760

Method: X-RAY DIFFRACTION D_max: 53.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rfm
deposition_date	2025-06-04
title	Crystal structure of the metallo-beta-lactamase VIM-1 with 1760
keywords	Inhibitor, Complex, Lactamase, HYDROLASE; 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	17.26 Å
rg_electron	15.93 Å
i0	11774100.00
molecular_weight	25002.0 kDa
excluded_volume	30972 Å³
envelope_volume	33989 Å³
shell_volume	17300 Å³
envelope_diameter	54.4 Å
shell_rg	22.64 Å
envelope_rg	16.25 Å
shape_rg	15.89 Å
total_rg	17.11 Å
total_atoms	3436
n_residues	232
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	53.4 Å
rg_real	17.12 Å
rg_real_error	0.22 Å
i0_real	1.1770e+07
i0_real_error	1.1650e+05
rg_reciprocal	17.14 Å
i0_reciprocal	11770000.0000
total_estimate	0.8935
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.5 Å
skewness	0.076
kurtosis	-0.459
angular_range	— – 0.4600 Å⁻¹
current_alpha	0.0000
highest_alpha	3816000.0000
n_real_points	77
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.879; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.994

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Beta-lactamase VIM-1
formula_weight	25434.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4365

SGEPSGEYPTVNEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEAEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSANVLYGGCAVHELSSTSAGNVADADLAEWPTSVERIQKHYPEAEVVIPGHGLPGGLDLLQHTANVVKAHKNRSVAE

Source

organism	Pseudomonas aeruginosa
ncbi_taxonomy_id	287
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	3-[3-fluoranyl-4-(methylsulfonylmethyl)phenyl]-4-methyl-5-phenyl-1~{H}-pyrrole-2-carboxylic acid
formula_weight	387.4 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	266

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6. Citations (1)

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length_a	39.398 Å
length_b	67.771 Å
length_c	40.118 Å
angle_alpha	90.00 °
angle_beta	93.17 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.050 Å
resolution_low	40.060 Å
r_factor	0.1134
r_work	0.1124
r_free	0.1324

fit	/app/data/saxs_computation/rf/9rfm/9rfm.fit
pddf	/app/data/pr_computation/rf/9rfm/9rfm.pr.out
profile	/app/data/saxs_computation/rf/9rfm/9rfm.dat