SAXSdb — 6vbc

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

Probable peptidoglycan D,D-transpeptidase PenA

Neisseria gonorrhoeae

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 237–575	Not recorded	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 1.55 Å R-free 0.200

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 6VBC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6VBD Crystal structure of transpeptidase domain of PBP2 from Neisseria gonorrhoeae cephalosporin-resistant strain H041 acylated by ceftriaxone Deposited 2019-12-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 237–575（339 aa）	Not recorded	CEF CEFOTAXIME, C3' cleaved, open, bound form × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.3；291 K；40% PEG 600, 0.1M CHES	Resolution 1.80 Å R-free 0.195
8VBZ Crystal structure of the transpeptidase domain of a S310A mutant of PBP2 from Neisseria gonorrhoeae strain H041 Deposited 2023-12-13	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 237–575（339 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；32-40% PEG 600, 0.1 M CHES	Resolution 1.90 Å R-free 0.211
8VEN Crystal structure of transpeptidase domain of PBP2 from Neisseria gonorrhoeae cephalosporin-resistant strain H041 in complex with cefoperazone Deposited 2023-12-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 237–575（339 aa）	Not recorded	A1ADP (2R,4R)-2-[(1R)-1-{[(2R)-2-[(4-ethyl-2,3-dioxopiperazine-1-carbonyl)amino]-2-(4-hydroxyphenyl)acetyl]amino}-2-oxoethyl]-5-methylidene-1,3-thiazinane-4-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；32-40% PEG 600, 0.1 M CHES	Resolution 1.80 Å R-free 0.201
8VEP Crystal structure of transpeptidase domain of PBP2 from Neisseria gonorrhoeae cephalosporin-resistant strain H041 acylated by piperacillin Deposited 2023-12-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 237–575（339 aa）	Not recorded	JPP Piperacillin (Open Form) × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.8；291 K；32-40% PEG 600, 0.1 M CHES	Resolution 2.00 Å R-free 0.206
8VEQ Crystal structure of transpeptidase domain of PBP2 from Neisseria gonorrhoeae cephalosporin-resistant strain H041 in complex with azlocillin Deposited 2023-12-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 237–575（339 aa）	Not recorded	59H (2R,4S)-5,5-dimethyl-2-[(1R)-2-oxo-1-{[(2R)-2-{[(2-oxoimidazolidin-1-yl)carbonyl]amino}-2-phenylacetyl]amino}ethyl]-1,3-thiazolidine-4-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.8；291 K；32-40% PEG 600, 0.1 M CHES	Resolution 2.40 Å R-free 0.250
9OSK Crystal structure of the transpeptidase domain of a Y422A mutant of PBP2 from Neisseria gonorrhoeae strain H041 Deposited 2025-05-24	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 237–575（339 aa）	Mutation：Y422A	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.60 Å R-free 0.253
9OSL Crystal structure of the transpeptidase domain of a Y422A mutant of PBP2 from Neisseria gonorrhoeae strain H041 acylated by ceftriaxone Deposited 2025-05-24	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 237–575（339 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å R-free 0.243
9Z5T Crystal structure of the transpeptidase domain of PBP2 from the Neisseria gonorrhoeae cephalosporin-resistant strain H041 in complex with boronate inhibitor VNRX-14079 Deposited 2025-11-12	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 237–575（339 aa）	Not recorded	A1C02 (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 × 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 2.10 Å R-free 0.236

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	F2Z7K9_NEIGO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–330； UniProt 237–575

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	6vbc
Deposition date deposition_date	2019-12-18
Structure title title	Crystal structure of transpeptidase domain of PBP2 from Neisseria gonorrhoeae cephalosporin-resistant strain H041
Keywords keywords	PENICILLIN-BINDING PROTEIN, ANTIBIOTIC RESISTANCE, TRANSPEPTIDASE DOMAIN, 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	19.50 Å
Radius of gyration Rg (electron density) rg_electron	18.41 Å
Forward intensity I(0) i0	19920400.00
Molecular weight molecular_weight	34839.0 kDa
Excluded volume excluded_volume	44024 Å³
Envelope volume envelope_volume	49070 Å³
Hydration-shell volume shell_volume	21533 Å³
Envelope diameter envelope_diameter	59.0 Å
Shell Rg shell_rg	25.45 Å
Envelope Rg envelope_rg	18.72 Å
Shape Rg shape_rg	18.42 Å
Total Rg total_rg	19.34 Å
Total atoms total_atoms	2453
Residues n_residues	324
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	59.5 Å
Rg (real space) rg_real	19.32 Å
Rg uncertainty (real space) rg_real_error	0.21 Å
I(0) (real space) i0_real	1.9920e+07
I(0) uncertainty (real space) i0_real_error	2.1540e+05
Rg (reciprocal space) rg_reciprocal	19.35 Å
I(0) (reciprocal space) i0_reciprocal	19920000.0000
Solution quality estimate total_estimate	0.8975
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.0 Å
Skewness Skewness skewness	0.073
Kurtosis Kurtosis kurtosis	-0.450
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6045000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.987

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6vbca1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
Family Family family	e.3.1.0 — automated matches

Domain ID domain_id	d6vbca2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	6vbcA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

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8. Citations (1)

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Unit-cell length a length_a	50.429 Å
Unit-cell length b length_b	61.329 Å
Unit-cell length c length_c	108.961 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	31.690 Å
R factor r_factor	0.1792
R_work r_work	0.1782
R_free r_free	0.2003

Description description	Probable peptidoglycan D,D-transpeptidase PenA
Molecular weight formula_weight	35361.5 kDa
EC 编号 ec_number	3.4.16.4
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2657

Crystal structure of transpeptidase domain of PBP2 from Neisseria gonorrhoeae cephalosporin-resistant strain H041

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

Probable peptidoglycan D,D-transpeptidase PenA

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Neisseria gonorrhoeae
NCBI Class编号 ncbi_taxonomy_id	485
宿主生物 host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	153

fit	/app/data/saxs_computation/vb/6vbc/6vbc.fit
pddf	/app/data/pr_computation/vb/6vbc/6vbc.pr.out
profile	/app/data/saxs_computation/vb/6vbc/6vbc.dat