3qi0

Structural, thermodynamic and kinetic analysis of the picomolar binding affinity interaction of the beta-lactamase inhibitor protein-II (BLIP-II) with class A beta-lactamases

Method: X-RAY DIFFRACTION

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

Beta-lactamase inhibitory protein II

Streptomyces exfoliatus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SULFATE ION × 7 water × 1	Consistent with protein count
10	Protein homooligomer	Homooligomer	Protein 6	SULFATE ION × 35 water × 6	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	SULFATE ION × 8 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	SULFATE ION × 4 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	SULFATE ION × 6 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	SULFATE ION × 8 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	SULFATE ION × 2 water × 1	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 8 water × 2	Consistent with protein count
8	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 12 water × 2	Consistent with protein count
9	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 15 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O87916_STREX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–271； UniProt 41–311 Author chain B； PDBConstruct 1–271； UniProt 41–311 Author chain C； PDBConstruct 1–271； UniProt 41–311 Author chain D； PDBConstruct 1–271； UniProt 41–311 Author chain E； PDBConstruct 1–271； UniProt 41–311 Author chain F； PDBConstruct 1–271； UniProt 41–311

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	3qi0
Deposition date deposition_date	2011-01-26
Structure title title	Structural, thermodynamic and kinetic analysis of the picomolar binding affinity interaction of the beta-lactamase inhibitor protein-II (BLIP-II) with class A beta-lactamases
Keywords keywords	enzyme-inhibitor complex, BSGC, beta-propeller, beta-lactamase, protein:protein interaction, HYDROLASE INHIBITOR; HYDROLASE INHIBITOR
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.

3qi0__assembly_2__model_1

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

Download this curve (.dat)

3qi0__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3qi0__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	18.54 Å
Rg (electron density)	17.25 Å
Total Rg	18.36 Å
Atom count	1944
Residues	268
Excluded volume	33821 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3qi0__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3qi0__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3qi0__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3qi0__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3qi0__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3qi0__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3qi0__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`3qi0__assembly_8__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`3qi0__assembly_9__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`3qi0__assembly_10__model_1`	hexameric （6）	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 (3)

Entity 1 Entity 1 polymer

Description description	Beta-lactamase inhibitory protein II
Molecular weight formula_weight	28360.9 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	11817

ATSVVAWGGNNDWGEATVPAEAQSGVDAIAGGYFHGLALKGGKVLGWGANLNGQLTMPAATQSGVDAIAAGNYHSLALKDGEVIAWGGNEDGQTTVPAEARSGVDAIAAGAWASYALKDGKVIAWGDDSDGQTTVPAEAQSGVTALDGGVYTALAVKNGGVIAWGDNYFGQTTVPAEAQSGVDDVAGGIFHSLALKDGKVIAWGDNRYKQTTVPTEALSGVSAIASGEWYSLALKNGKVIAWGSSRTAPSSVQSGVSSIEAGPNAAYALKGGSGSGHHHHHH

Source Source

Source organism organism	Streptomyces exfoliatus
Common name common_name	Streptomyces hydrogenans
NCBI taxonomy ID ncbi_taxonomy_id	1905
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	35

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	199

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3qi0a_
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.5 — RCC1/BLIP-II
Family Family family	b.69.5.2 — beta-lactamase inhibitor protein-II, BLIP-II

Domain ID domain_id	d3qi0b_
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.5 — RCC1/BLIP-II
Family Family family	b.69.5.2 — beta-lactamase inhibitor protein-II, BLIP-II

Domain ID domain_id	d3qi0c_
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.5 — RCC1/BLIP-II
Family Family family	b.69.5.2 — beta-lactamase inhibitor protein-II, BLIP-II

Domain ID domain_id	d3qi0d_
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.5 — RCC1/BLIP-II
Family Family family	b.69.5.2 — beta-lactamase inhibitor protein-II, BLIP-II

Domain ID domain_id	d3qi0e_
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.5 — RCC1/BLIP-II
Family Family family	b.69.5.2 — beta-lactamase inhibitor protein-II, BLIP-II

Domain ID domain_id	d3qi0f_
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.5 — RCC1/BLIP-II
Family Family family	b.69.5.2 — beta-lactamase inhibitor protein-II, BLIP-II

CATH v4.4 (6 domains)

Domain ID domain_id	3qi0A00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	30 — Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II

Domain ID domain_id	3qi0B00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	30 — Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II

Domain ID domain_id	3qi0C00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	30 — Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II

Domain ID domain_id	3qi0D00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	30 — Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II

Domain ID domain_id	3qi0E00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	30 — Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II

Domain ID domain_id	3qi0F00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	30 — Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II

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Unit-cell length a length_a	114.606 Å
Unit-cell length b length_b	114.737 Å
Unit-cell length c length_c	173.827 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	24

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

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1976
R_work r_work	0.1952
R_free r_free	0.2425

Structural, thermodynamic and kinetic analysis of the picomolar binding affinity interaction of the beta-lactamase inhibitor protein-II (BLIP-II) with class A beta-lactamases

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

Beta-lactamase inhibitory protein II

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

3qi0__assembly_2__model_1

3qi0__assembly_2__model_1 | I(q)

3qi0__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Structural, thermodynamic and kinetic analysis of the picomolar binding affinity interaction of the beta-lactamase inhibitor protein-II (BLIP-II) with class A beta-lactamases

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

Beta-lactamase inhibitory protein II

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

3qi0__assembly_2__model_1

3qi0__assembly_2__model_1 | I(q)

3qi0__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)