← Back to search

9z0w

Crystal structure of Neisseria gonorrhoeae penicillin-binding protein 2 from strain FA19 containing six resistance mutations

Method: X-RAY DIFFRACTION D_max: 89.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9z0w
deposition_date	2025-11-03
last_revision	2026-03-04
title	Crystal structure of Neisseria gonorrhoeae penicillin-binding protein 2 from strain FA19 containing six resistance mutations
keywords	PENICILLIN-BINDING PROTEIN, TRANSPEPTIDASE DOMAIN, N. GONORRHOEAE, ANTIBIOTIC RESISTANCE, HYDROLASE; HYDROLASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	27.86 Å
rg_electron	27.11 Å
i0	76954400.00
molecular_weight	69298.0 kDa
excluded_volume	87139 Å³
envelope_volume	103710 Å³
shell_volume	31868 Å³
envelope_diameter	93.5 Å
shell_rg	34.42 Å
envelope_rg	27.24 Å
shape_rg	27.11 Å
total_rg	27.84 Å
total_atoms	4881
n_residues	641
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

▼

3. P(r) Analysis (GNOM)

dmax	89.9 Å
rg_real	27.88 Å
rg_real_error	0.47 Å
i0_real	7.6950e+07
i0_real_error	1.0650e+06
rg_reciprocal	27.88 Å
i0_reciprocal	76950000.0000
total_estimate	0.8894
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	30.0 Å
skewness	0.369
kurtosis	-0.446
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	23270000.0000
n_real_points	58
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.873; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.947

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

Entity 1 polymer

description	Penicillin-binding protein 2
formula_weight	35391.4 kDa
ec_number	3.4.16.4
mutation	A311V, I312M, V316P, F504L, N512Y, G545S
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4957

GSGGALSLDQRIQTLAYEELNKAVEYHQAKAGTVVVLDARTGEILALANTPGRNRAVTDMIEPGSVMKPFPIAKALDAGKTDLNERLNTQPYKIGPSPVRDTHVYPSLDVRGIMQKSSNVGTSKLSARFGAEEMYDFYHELGIGVRMHSGFPGETAGLLRNWRRWRPIEQATMSFGYGLQLSLLQLARAYTALTHDGVLLPLSFEKQAVAPQGKRIFKESTAREVRNLMVSVTEPGGTGTAGAVDGFDVGAKTGTARKLVNGRYADYKHVATFIGFAPAKNPRVIVAVTIDEPTANGYYSGVVAGPPFKKIMGGSLNILGISPTKPLTA

Source

organism	Neisseria gonorrhoeae FA19
ncbi_taxonomy_id	528352
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	1

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	76

▶

6. Citations (1)

▶

length_a	44.883 Å
length_b	77.048 Å
length_c	87.778 Å
angle_alpha	90.00 °
angle_beta	91.95 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.150 Å
resolution_low	35.850 Å
r_factor	0.1904
r_work	0.1870
r_free	0.2462

fit	/app/data/saxs_computation/z0/9z0w/9z0w.fit
pddf	/app/data/pr_computation/z0/9z0w/9z0w.pr.out
profile	/app/data/saxs_computation/z0/9z0w/9z0w.dat

Crystal structure of Neisseria gonorrhoeae penicillin-binding protein 2 from strain FA19 containing six resistance mutations

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