SAXSdb — 9xfy

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

Beta-lactamase

Yersinia enterocolitica

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 1–294	Not recorded	2RG (2S,3R,4S)-4-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-2-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid × 1 PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M TRIS hydrochloride pH 8.5, 2.0 M Ammonium phosphate monobasic	Resolution 1.70 Å R-free 0.230

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 9XFY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8IWV Crystal structure of BlaA-1 APO Deposited 2023-03-31	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–294（294 aa）	Not recorded	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M TRIS hydrochloride pH 8.5, 2.0 M Ammonium phosphate monobasic	Resolution 2.40 Å R-free 0.235
9VGV Crystal Structure of BlaA beta-lactamase in complex with the Antifungal Agent Tavaborole. Deposited 2025-06-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 34–294（261 aa）	Not recorded	A1CF8 Tavaborole × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M TRIS hydrochloride pH 8.5, 2.0 M Ammonium phosphate monobasic	Resolution 2.50 Å R-free 0.269
9XFW Crystal structure of Class A beta-lactamase BlaA in complex with Meropenem (Imine form) Deposited 2025-10-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–294（294 aa）	Not recorded	DWZ (2S,3R,4S)-4-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-2-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M TRIS hydrochloride pH 8.5, 2.0 M Ammonium phosphate monobasic	Resolution 2.00 Å R-free 0.271
9XFX Crystal structure of Class A beta-lactamase BlaA in complex with Tebipenem (imine form) Deposited 2025-10-29	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–294（294 aa）	Not recorded	A1MCI TEBIPENEM, BOUND FORM × 1 EDO 1,2-ETHANEDIOL × 1 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M TRIS hydrochloride pH 8.5, 2.0 M Ammonium phosphate monobasic	Resolution 1.50 Å R-free 0.204

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

View Construct and Data Evidence

UniProt name	BLAC_YEREN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–294； UniProt 1–294

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	9xfy
Deposition date deposition_date	2025-10-29
最后修订 last_revision	2025-11-12
Structure title title	Crystal structure of Class A beta-lactamase BlaA in complex with ertapenem (imine form)
Keywords keywords	Imine tautomer, Carbapenemase, Acyl enzyme complex, 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	18.85 Å
Radius of gyration Rg (electron density) rg_electron	17.68 Å
Forward intensity I(0) i0	15875000.00
Molecular weight molecular_weight	29264.0 kDa
Excluded volume excluded_volume	36336 Å³
Envelope volume envelope_volume	40299 Å³
Hydration-shell volume shell_volume	18810 Å³
Envelope diameter envelope_diameter	61.6 Å
Shell Rg shell_rg	24.23 Å
Envelope Rg envelope_rg	18.10 Å
Shape Rg shape_rg	17.68 Å
Total Rg total_rg	18.59 Å
Total atoms total_atoms	2052
Residues n_residues	262
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	60.7 Å
Rg (real space) rg_real	18.76 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	1.5870e+07
I(0) uncertainty (real space) i0_real_error	1.8480e+05
Rg (reciprocal space) rg_reciprocal	18.77 Å
I(0) (reciprocal space) i0_reciprocal	15880000.0000
Solution quality estimate total_estimate	0.8874
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.4 Å
Skewness Skewness skewness	0.229
Kurtosis Kurtosis kurtosis	-0.276
Angular range angular_range	— – 0.4200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3899000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.992

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Beta-lactamase
Molecular weight formula_weight	31966.6 kDa
EC 编号 ec_number	3.5.2.6
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2264

MKHSSLRRSLLLAGITLPLVSFALPAWANALPASVDKQLAELERNANGRLGVAMINTGNGTKILYRAAQRFPFCSTFKFMLAAAVLDQSQSQPNLLNKHINYHESDLLSYAPITRKNLAHGMTVSELCAATIQYSDNTAANLLIKELGGLAAVNQFARSIGDQMFRLDRWEPDLNTARPNDPRDTTTPAAMAASMNKLVLGDALRPAQRSQLAVWLKGNTTGDATIRAGAPTDWIVGDKTGSGDYGTTNDIAVLWPTKGAPIVLVVYFTQREKDAKPRRDVLASVTKIILSQIS

来源 Source

来源生物 organism	Yersinia enterocolitica
NCBI Class编号 ncbi_taxonomy_id	630
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	;(2S,3R,4S)-4-({(3S,5S)-5-[(3-carboxyphenyl)carbamoyl]pyrrolidin-3-yl}sulfanyl)-2-[(1S,2R)-1-formyl-2-hydroxypropyl]-3-methyl-3,4-dihydro-2H-pyrrole-5-carboxylic acid ;
Molecular weight formula_weight	477.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	212

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8. Citations (1)

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Unit-cell length a length_a	91.743 Å
Unit-cell length b length_b	72.818 Å
Unit-cell length c length_c	43.700 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.78 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	24.663 Å
R factor r_factor	—
R_work r_work	0.1936
R_free r_free	0.2298

fit	/app/data/saxs_computation/xf/9xfy/9xfy.fit
pddf	/app/data/pr_computation/xf/9xfy/9xfy.pr.out
profile	/app/data/saxs_computation/xf/9xfy/9xfy.dat

Crystal structure of Class A beta-lactamase BlaA in complex with ertapenem (imine form)

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

Beta-lactamase

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