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9z5t

;Crystal structure of the transpeptidase domain of PBP2 from the Neisseria gonorrhoeae cephalosporin-resistant strain H041 in complex with boronate inhibitor VNRX-14079 ;

Method: X-RAY DIFFRACTION D_max: 59.1 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9z5t
deposition_date	2025-11-12
title	;Crystal structure of the transpeptidase domain of PBP2 from the Neisseria gonorrhoeae cephalosporin-resistant strain H041 in complex with boronate inhibitor VNRX-14079 ;
keywords	Neisseria gonorrhoeae, cephalosporin resistance, Penicillin-binding protein 2, Boronate inhibitor, ligase; LIGASE
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	19.32 Å
rg_electron	18.41 Å
i0	39777000.00
molecular_weight	32638.0 kDa
excluded_volume	31518 Å³
envelope_volume	49588 Å³
shell_volume	21707 Å³
envelope_diameter	59.7 Å
shell_rg	25.53 Å
envelope_rg	18.73 Å
shape_rg	18.42 Å
total_rg	19.11 Å
total_atoms	2473
n_residues	321
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	59.1 Å
rg_real	19.17 Å
rg_real_error	0.24 Å
i0_real	3.9780e+07
i0_real_error	4.9520e+05
rg_reciprocal	19.19 Å
i0_reciprocal	39780000.0000
total_estimate	0.7454
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	25.0 Å
skewness	0.111
kurtosis	-0.440
angular_range	— – 0.4100 Å⁻¹
current_alpha	0.0000
highest_alpha	9761000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 0.356; Positv: 1.000; Valcen: 0.984; Smooth: 0.926

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	Probable peptidoglycan D,D-transpeptidase PenA
formula_weight	35361.5 kDa
ec_number	3.4.16.4
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2562

GSGGALSLDQRIQTLAYEELNKAVEYHQAKAGTVVVLDARTGEILALVNTPGRNRAVTDMIEPGSVMKPFPIAKALDSGKVDTTDTFNTLPYKIGPATVQDTHVYPTLDVRGIMQKSSNVGTSKLSAMFTPKEMYDFYHDLGVGVRMHSGFPGESAGVLRNWRKWRPIEQATMSFGYGLQLSLLQLARAYTVLTHDGELLPVSFEKQAVAPKGKRVIKASTAKKVRELMVSVTEAGGSGIAGAVDGFDVGAKTGTARKLVNGRYVDYKHVATFIGFAPAKNPRVIVAVTIDEPTANGYYSGVVTGPVFKQVMGGSLNILGVSPTKPLTNV

Source

organism	Neisseria gonorrhoeae
ncbi_taxonomy_id	485
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	;(3R)-7-fluoro-3-{[(2R)-2-(3-fluoro-4-phosphonophenyl)-2-{[3-(methanesulfonyl)-2-oxoimidazolidine-1-carbonyl]amino}acetyl]amino}-2-hydroxy-3,4-dihydro-2H-1,2-benzoxaborinine-8-carboxylic acid ;
formula_weight	646.3 kDa
src_method	nat
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	77

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6. Citations (1)

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length_a	49.865 Å
length_b	60.151 Å
length_c	111.023 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.100 Å
resolution_low	40.830 Å
r_factor	0.1930
r_work	0.1910
r_free	0.2360

fit	/app/data/saxs_computation/z5/9z5t/9z5t.fit
pddf	/app/data/pr_computation/z5/9z5t/9z5t.pr.out
profile	/app/data/saxs_computation/z5/9z5t/9z5t.dat

;Crystal structure of the transpeptidase domain of PBP2 from the Neisseria gonorrhoeae cephalosporin-resistant strain H041 in complex with boronate inhibitor VNRX-14079 ;

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