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9rfg

Crystal structure of the metallo-beta-lactamase VIM-1 with 1476

Method: X-RAY DIFFRACTION D_max: 54.1 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rfg
deposition_date	2025-06-04
title	Crystal structure of the metallo-beta-lactamase VIM-1 with 1476
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	17.03 Å
rg_electron	16.01 Å
i0	21431800.00
molecular_weight	23434.0 kDa
excluded_volume	22565 Å³
envelope_volume	34201 Å³
shell_volume	17348 Å³
envelope_diameter	55.7 Å
shell_rg	22.72 Å
envelope_rg	16.32 Å
shape_rg	15.98 Å
total_rg	16.83 Å
total_atoms	1784
n_residues	234
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	54.1 Å
rg_real	16.90 Å
rg_real_error	0.21 Å
i0_real	2.1430e+07
i0_real_error	2.3960e+05
rg_reciprocal	16.91 Å
i0_reciprocal	21430000.0000
total_estimate	0.8872
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	22.1 Å
skewness	0.106
kurtosis	-0.441
angular_range	— – 0.4650 Å⁻¹
current_alpha	0.0000
highest_alpha	6975000.0000
n_real_points	77
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.999

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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	2329

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-[3,5-bis(chloranyl)phenyl]-4-ethyl-5-phenyl-1~{H}-pyrrole-2-carboxylic acid
formula_weight	360.2 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	299

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6. Citations (3)

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length_a	39.338 Å
length_b	67.652 Å
length_c	40.147 Å
angle_alpha	90.00 °
angle_beta	93.35 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.150 Å
resolution_low	40.080 Å
r_factor	0.1382
r_work	0.1368
r_free	0.1660

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