SAXSdb — 3qi0

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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	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 41–311	Fragment：unp residues 41-311	SO4 SULFATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.0 M ammonium sulfate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.243
10	Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 41–311 Chain B； UniProt 41–311 Chain C； UniProt 41–311 Chain D； UniProt 41–311 Chain E； UniProt 41–311 Chain F； UniProt 41–311	Fragment：unp residues 41-311	SO4 SULFATE ION × 35	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.0 M ammonium sulfate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.243
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 41–311	Fragment：unp residues 41-311	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.0 M ammonium sulfate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.243
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 41–311	Fragment：unp residues 41-311	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.0 M ammonium sulfate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.243
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 41–311	Fragment：unp residues 41-311	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.0 M ammonium sulfate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.243
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 41–311	Fragment：unp residues 41-311	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.0 M ammonium sulfate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.243
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 41–311	Fragment：unp residues 41-311	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.0 M ammonium sulfate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.243
7	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 41–311 Chain F； UniProt 41–311	Fragment：unp residues 41-311	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.0 M ammonium sulfate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.243
8	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 41–311 Chain C； UniProt 41–311	Fragment：unp residues 41-311	SO4 SULFATE ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.0 M ammonium sulfate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.243
9	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 41–311 Chain E； UniProt 41–311	Fragment：unp residues 41-311	SO4 SULFATE ION × 15	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；2.0 M ammonium sulfate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.243

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 3QI0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1JTD Crystal structure of beta-lactamase inhibitor protein-II in complex with TEM-1 beta-lactamase Deposited 2001-08-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 39–311（273 aa）	Not recorded	CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；PEG8000, calcium acetate, sodium cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.230
3QHY 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 Deposited 2011-01-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 41–311（271 aa） Fragment：unp residues 41-311	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；298 K；0.1M Bicine, 13 % PEG 10,000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.06 Å R-free 0.217
9T9P Adenosine receptor A2a (A2AR)-beta-lactamase fusion bound to beta-lactamase inhibitory protein II (BLIPII) and ZM241385 Deposited 2025-11-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 41–311（271 aa）	Not recorded	ZMA 4-{2-[(7-amino-2-furan-2-yl[1,2,4]triazolo[1,5-a][1,3,5]triazin-5-yl)amino]ethyl}phenol × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

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

Radius of gyration Rg (Guinier) rg_guinier	37.79 Å
Radius of gyration Rg (electron density) rg_electron	37.37 Å
Forward intensity I(0) i0	458653000.00
Molecular weight molecular_weight	165110.0 kDa
Excluded volume excluded_volume	202500 Å³
Envelope volume envelope_volume	258110 Å³
Hydration-shell volume shell_volume	57213 Å³
Envelope diameter envelope_diameter	133.6 Å
Shell Rg shell_rg	43.68 Å
Envelope Rg envelope_rg	36.82 Å
Shape Rg shape_rg	37.31 Å
Total Rg total_rg	37.93 Å
Total atoms total_atoms	11618
Residues n_residues	1611
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	120.8 Å
Rg (real space) rg_real	37.74 Å
Rg uncertainty (real space) rg_real_error	0.85 Å
I(0) (real space) i0_real	4.5870e+08
I(0) uncertainty (real space) i0_real_error	7.3770e+06
Rg (reciprocal space) rg_reciprocal	37.78 Å
I(0) (reciprocal space) i0_reciprocal	458700000.0000
Solution quality estimate total_estimate	0.6666
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	46.0 Å
Skewness Skewness skewness	0.323
Kurtosis Kurtosis kurtosis	-0.266
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	99280000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 0.080; Positv: 1.000; Valcen: 0.996; Smooth: 0.694

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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	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

来源 Source

来源生物 organism	Streptomyces exfoliatus
通用名 common_name	Streptomyces hydrogenans
NCBI Class编号 ncbi_taxonomy_id	1905
宿主生物 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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7. 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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8. Citations (1)

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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

fit	/app/data/saxs_computation/qi/3qi0/3qi0.fit
pddf	/app/data/pr_computation/qi/3qi0/3qi0.pr.out
profile	/app/data/saxs_computation/qi/3qi0/3qi0.dat

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

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