SAXSdb — 9w7p

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

Beta-lactamase SME-1

Serratia marcescens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	(3~{R})-2-oxidanyl-3-(propanoylamino)-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	(3~{R})-2-oxidanyl-3-(propanoylamino)-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BLAS1_SERMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–267； UniProt 28–294 Author chain B； PDBConstruct 1–267； UniProt 28–294

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	9w7p
Deposition date deposition_date	2025-08-06
Structure title title	Crystal Structure of Ledaborbactam in complex with SME-1 class A Carbapenemase
Keywords keywords	Acyl Enzyme Complex, Carbapenemase, BATSA, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9w7p__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9w7p__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9w7p__assembly_2__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	18.73 Å
Rg (electron density)	17.75 Å
Total Rg	18.72 Å
Atom count	2078
Residues	267
Excluded volume	36738 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9w7p__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9w7p__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Beta-lactamase SME-1
Molecular weight formula_weight	29386.2 kDa
EC 编号 ec_number	3.5.2.6
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	4327

NKSDAAAKQIKKLEEDFDGRIGVFAIDTGSGNTFGYRSDERFPLCSSFKGFLAAAVLERVQQKKLDINQKVKYESRDLEYHSPITTKYKGSGMTLGDMASAALQYSDNGATNIIMERFLGGPEGMTKFMRSIGDNEFRLDRWELELNTAIPGDKRDTSTPKAVANSLNKLALGNVLNAKVKAIYQNWLKGNTTGDARIRASVPADWVVGDKTGSCGAYGTANDYAVIWPKNRAPLIVSIYTTRKSKDDKHSDKTIAEASRIAIQAID

Source Source

Source organism organism	Serratia marcescens
NCBI taxonomy ID ncbi_taxonomy_id	615
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	(3~{R})-2-oxidanyl-3-(propanoylamino)-3,4-dihydro-1,2-benzoxaborinine-8-carboxylic acid
Molecular weight formula_weight	263.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	164

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Unit-cell length a length_a	36.391 Å
Unit-cell length b length_b	50.465 Å
Unit-cell length c length_c	130.588 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.72 °
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	2.200 Å
Low-resolution limit resolution_low	21.577 Å
R factor r_factor	—
R_work r_work	0.1930
R_free r_free	0.2547

Crystal Structure of Ledaborbactam in complex with SME-1 class A Carbapenemase

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

Beta-lactamase SME-1

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9w7p__assembly_2__model_1

9w7p__assembly_2__model_1 | I(q)

9w7p__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

Crystal Structure of Ledaborbactam in complex with SME-1 class A Carbapenemase

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

Beta-lactamase SME-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9w7p__assembly_2__model_1

9w7p__assembly_2__model_1 | I(q)

9w7p__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)