SAXSdb — 1k9b

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

BOWMAN-BIRK TYPE PROTEINASE INHIBITOR

OrganismNot specified

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 45–102	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.6；289 K；PEG 4000, ammonium sulfate, pH 7.6, VAPOR DIFFUSION, SITTING DROP at 289K	Resolution 2.80 Å R-free 0.308

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 1K9B	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BBI THREE-DIMENSIONAL STRUCTURE OF SOYBEAN TRYPSIN(SLASH)CHYMOTRYPSIN BOWMAN-BIRK INHIBITOR IN SOLUTION Deposited 1991-09-19	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 40–110（71 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1D6R CRYSTAL STRUCTURE OF CANCER CHEMOPREVENTIVE BOWMAN-BIRK INHIBITOR IN TERNARY COMPLEX WITH BOVINE TRYPSIN AT 2.3 A RESOLUTION. STRUCTURAL BASIS OF JANUS-FACED SERINE PROTEASE INHIBITOR SPECIFICITY Deposited 1999-10-15	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain I 45–102（58 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；PROTEIN SOLUTION: TRIS/CL, CACL2, MGSO4.7H2O, NAN3 PLUS PRECIPITANT PRECIPITANTS: (NH4)2SO4, MDP, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K	Resolution 2.30 Å R-free 0.226
2BBI THREE-DIMENSIONAL STRUCTURE OF SOYBEAN TRYPSIN(SLASH)CHYMOTRYPSIN BOWMAN-BIRK INHIBITOR IN SOLUTION Deposited 1991-09-19	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 40–110（71 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
5J4Q alpha-chymotrypsin from bovine pancreas in complex with Bowman-Birk inhibitor from soybean Deposited 2016-04-01	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 40–110（71 aa） Fragment：UNP residues 40-110	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；291 K；12%(w/v) PEG 20000, 0.1M MES, pH6.5	Resolution 2.30 Å R-free 0.267
5J4S alpha-chymotrypsin from bovine pancreas in complex with a modified Bowman-Birk inhibitor from soybean Deposited 2016-04-01	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 40–110（71 aa） Fragment：UNP residues 40-110	Mutation：M27L,A22T,L42F,Y45I,A47P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；10mM nickel chloride, 0.1M Tris-HCl, pH8.5, 20% (w/v) PEG MME 2000	Resolution 2.10 Å R-free 0.241

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IBB1_SOYBN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–58； UniProt 45–102

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	1k9b
Deposition date deposition_date	2001-10-29
Structure title title	Crystal structure of the bifunctional soybean Bowman-Birk inhibitor at 0.28 nm resolution. Structural peculiarities in a folded protein conformation
Keywords keywords	TRIPPLE-STRANDED BETA HAIRPIN, DOUBLE-HEADED, 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	12.32 Å
Radius of gyration Rg (electron density) rg_electron	11.95 Å
Forward intensity I(0) i0	1163360.00
Molecular weight molecular_weight	6205.0 kDa
Excluded volume excluded_volume	7315 Å³
Envelope volume envelope_volume	8811 Å³
Hydration-shell volume shell_volume	7075 Å³
Envelope diameter envelope_diameter	45.7 Å
Shell Rg shell_rg	16.36 Å
Envelope Rg envelope_rg	12.43 Å
Shape Rg shape_rg	12.04 Å
Total Rg total_rg	12.82 Å
Total atoms total_atoms	513
Residues n_residues	58
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	48.2 Å
Rg (real space) rg_real	12.40 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	1.1630e+06
I(0) uncertainty (real space) i0_real_error	1.4160e+04
Rg (reciprocal space) rg_reciprocal	12.40 Å
I(0) (reciprocal space) i0_reciprocal	1163000.0000
Solution quality estimate total_estimate	0.7857
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	13.4 Å
Skewness Skewness skewness	0.541
Kurtosis Kurtosis kurtosis	0.143
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	150300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.561; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.535; Smooth: 0.992

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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1k9ba_
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.13 — Bowman-Birk inhibitor, BBI
Family Family family	g.3.13.1 — Bowman-Birk inhibitor, BBI

CATH v4.4 (1 domains)

Domain ID domain_id	1k9bA00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	69 — Cysteine Protease (Bromelain) Inhibitor, subunit H
Homologous superfamily homologous superfamily	10 — Cysteine Protease (Bromelain) Inhibitor, subunit H

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8. Citations (6)

;Crystal structure of the bifunctional soybean Bowman-Birk inhibitor at 0.28-nm resolution. Structural peculiarities in a folded protein conformation. ;

Eur.J.Biochem. (1996)

PMID: 8954162 · DOI: 10.1111/j.1432-1033.1996.0122r.x PRIMARY

;Crystal Structure of Cancer Chemopreventive Bowman-Birk Inhibitor in Ternary Complex with Bovine Trypsin at 2.3 Ao Resolution. Structural Basis of Janus-faced Serine Protease Inhibitor Specificity ;

J.Mol.Biol. (2000)

DOI: 10.1006/jmbi.2000.3677

;Mutational analysis of disulfide bonds in the trypsin-reactive subdomain of a Bowman-Birk-type inhibitor of trypsin and chymotrypsin. Cooperative versus autonomous refolding of subdomains ;

Eur.J.Biochem. (1998)

DOI: 10.1046/j.1432-1327.1998.2510854.x

Template-directed protein folding into a metastable state of increased activity

Eur.J.Biochem. (1995)

;A new and general procedure for refolding mutant Bowman-Birk-type proteinase inhibitors on trypsin-Sepharose as a matrix with complementary structure. ;

FEBS Lett. (1989)

DOI: 10.1016/0014-5793(89)80909-3

Chemical synthesis, molecular cloning and expression of gene coding for a Bowman-Birk-type proteinase inhibitor

Eur.J.Biochem. (1987)

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Unit-cell length a length_a	86.100 Å
Unit-cell length b length_b	86.100 Å
Unit-cell length c length_c	86.100 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 41 3 2
Space-group number int_tables_number	213
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.2210
R_free r_free	0.3080

Description description	BOWMAN-BIRK TYPE PROTEINASE INHIBITOR
Molecular weight formula_weight	6431.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	530

Crystal structure of the bifunctional soybean Bowman-Birk inhibitor at 0.28 nm resolution. Structural peculiarities in a folded protein conformation

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

BOWMAN-BIRK TYPE PROTEINASE INHIBITOR

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

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (6)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	17

fit	/app/data/saxs_computation/k9/1k9b/1k9b.fit
pddf	/app/data/pr_computation/k9/1k9b/1k9b.pr.out
profile	/app/data/saxs_computation/k9/1k9b/1k9b.dat