SAXSdb — 9z0x

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Penicillin-binding protein 2

Neisseria gonorrhoeae FA19

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 237–574	Mutation：A311V, I312M, V316P, T483S, F504L, N512Y, G545S	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9.3；291 K；40% PEG 600, 0.1 M CHES	Resolution 1.90 Å R-free 0.239
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 237–574	Mutation：A311V, I312M, V316P, T483S, F504L, N512Y, G545S	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9.3；291 K；40% PEG 600, 0.1 M CHES	Resolution 1.90 Å R-free 0.239

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9Z0X	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9Z0W Crystal structure of Neisseria gonorrhoeae penicillin-binding protein 2 from strain FA19 containing six resistance mutations Deposited 2025-11-03	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 237–574（338 aa）	Mutation：A311V, I312M, V316P, F504L, N512Y, G545S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.3；291 K；40% PEG 600, 0.1 M CHES	Resolution 2.15 Å R-free 0.246
9Z0W Crystal structure of Neisseria gonorrhoeae penicillin-binding protein 2 from strain FA19 containing six resistance mutations Deposited 2025-11-03	Different mutation/modification Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 237–574（338 aa）	Mutation：A311V, I312M, V316P, F504L, N512Y, G545S	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.3；291 K；40% PEG 600, 0.1 M CHES	Resolution 2.15 Å R-free 0.246
9Z0Y Crystal structure of Neisseria gonorrhoeae penicillin-binding protein 2 from strain FA19 containing seven resistance mutations and three epistatic mutations Deposited 2025-11-03	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 237–574（338 aa）	Mutation：A311V, I312M, V316P, T483S, F504L, N512Y, G545S, F462I, A437V, L447V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.3；291 K；40% PEG 600, 0.1M CHES	Resolution 1.46 Å R-free 0.188
9Z0Y Crystal structure of Neisseria gonorrhoeae penicillin-binding protein 2 from strain FA19 containing seven resistance mutations and three epistatic mutations Deposited 2025-11-03	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 237–574（338 aa）	Mutation：A311V, I312M, V316P, T483S, F504L, N512Y, G545S, F462I, A437V, L447V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.3；291 K；40% PEG 600, 0.1M CHES	Resolution 1.46 Å R-free 0.188

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0AB74EE38_NEIGO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–329； UniProt 237–574 Author chain B； PDBConstruct 6–329； UniProt 237–574

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9z0x
Deposition date deposition_date	2025-11-03
最后修订 last_revision	2026-03-04
Structure title title	Crystal structure of Neisseria gonorrhoeae penicillin-binding protein 2 from strain FA19 containing seven resistance mutations
Keywords keywords	PENICILLIN-BINDING PROTEIN, TRANSPEPTIDASE DOMAIN, N. GONORRHOEAE, ANTIBIOTIC RESISTANCE, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	27.85 Å
Radius of gyration Rg (electron density) rg_electron	27.08 Å
Forward intensity I(0) i0	77069600.00
Molecular weight molecular_weight	69383.0 kDa
Excluded volume excluded_volume	87252 Å³
Envelope volume envelope_volume	103550 Å³
Hydration-shell volume shell_volume	31804 Å³
Envelope diameter envelope_diameter	93.6 Å
Shell Rg shell_rg	34.46 Å
Envelope Rg envelope_rg	27.23 Å
Shape Rg shape_rg	27.09 Å
Total Rg total_rg	27.81 Å
Total atoms total_atoms	4887
Residues n_residues	642
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	90.3 Å
Rg (real space) rg_real	27.87 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	7.7070e+07
I(0) uncertainty (real space) i0_real_error	1.0270e+06
Rg (reciprocal space) rg_reciprocal	27.87 Å
I(0) (reciprocal space) i0_reciprocal	77070000.0000
Solution quality estimate total_estimate	0.8878
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.1 Å
Skewness Skewness skewness	0.367
Kurtosis Kurtosis kurtosis	-0.451
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	23500000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.866; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.948

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Penicillin-binding protein 2
Molecular weight formula_weight	35377.4 kDa
EC 编号 ec_number	3.4.16.4
Mutation mutation	A311V, I312M, V316P, T483S, F504L, N512Y, G545S
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5015

GSGGALSLDQRIQTLAYEELNKAVEYHQAKAGTVVVLDARTGEILALANTPGRNRAVTDMIEPGSVMKPFPIAKALDAGKTDLNERLNTQPYKIGPSPVRDTHVYPSLDVRGIMQKSSNVGTSKLSARFGAEEMYDFYHELGIGVRMHSGFPGETAGLLRNWRRWRPIEQATMSFGYGLQLSLLQLARAYTALTHDGVLLPLSFEKQAVAPQGKRIFKESTAREVRNLMVSVTEPGGSGTAGAVDGFDVGAKTGTARKLVNGRYADYKHVATFIGFAPAKNPRVIVAVTIDEPTANGYYSGVVAGPPFKKIMGGSLNILGISPTKPLTA

来源 Source

来源生物 organism	Neisseria gonorrhoeae FA19
NCBI Class编号 ncbi_taxonomy_id	528352
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	107

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8. Citations (1)

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Unit-cell length a length_a	44.556 Å
Unit-cell length b length_b	76.839 Å
Unit-cell length c length_c	87.478 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.37 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	35.750 Å
R factor r_factor	0.2017
R_work r_work	0.1998
R_free r_free	0.2388

fit	/app/data/saxs_computation/z0/9z0x/9z0x.fit
pddf	/app/data/pr_computation/z0/9z0x/9z0x.pr.out
profile	/app/data/saxs_computation/z0/9z0x/9z0x.dat

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Penicillin-binding protein 2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction