SAXSdb — 1bbp

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

BILIN BINDING PROTEIN

Pieris brassicae

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 16–188 Chain B； UniProt 16–188 Chain C； UniProt 16–188 Chain D； UniProt 16–188	Not recorded	BLV BILIVERDIN IX GAMMA CHROMOPHORE × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.00 Å

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 1BBP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1KXO ENGINEERED LIPOCALIN DIGA16 : APO-FORM Deposited 2002-02-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 16–189（174 aa）	Mutation：N1D, N21G, E28Q, K31A, N34D, S35H, V36I, E37T, N48R, H60S, I69S, K87S, L88Y, Y90I, K95Q, N97G, Y114F, K116S, Q125M, F127L, K135M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；298 K；0.1-M Hepes, 10% Isopropanole, 19% PEG 4000, pH = 7.8, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.289
1LKE ENGINEERED LIPOCALIN DIGA16 IN COMPLEX WITH DIGOXIGENIN Deposited 2002-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 16–189（174 aa）	Mutation：N1D, N21G, E28Q, K31A, N34D, S35H, V36I, E37T, N48R, H60S, I69S, K87S, L88Y, Y90I, K95Q, N97G, Y114F, K116S, Q125M, F127L, K135M	DOG DIGOXIGENIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.1-M HEPES, 10% ISOPROPANOL, 19% PEG 4000, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.248
1LNM ANTICALIN DIGA16 IN COMPLEX WITH DIGITOXIGENIN Deposited 2002-05-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 16–189（174 aa）	Mutation：N1D, N21G, E28Q, K31A, N34D, S35H, V36I, E37T, N48R, H60S, I69S, K87S, L88Y, Y90I, K95Q, N97G, Y114F, K116S, Q125M, F127L, K135M	DTX DIGITOXIGENIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；298 K；0.1-M hepes, 10% isopropanol, 19% peg 4000, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.245
1N0S ENGINEERED LIPOCALIN FLUA IN COMPLEX WITH FLUORESCEIN Deposited 2002-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 16–189（174 aa）	Not recorded	FLU 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；2.0 M (NH4)2SO4, 2% (w/v) PEG 400, 10 mM hepes/naoh, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 298 KK	Resolution 2.00 Å R-free 0.243
1N0S ENGINEERED LIPOCALIN FLUA IN COMPLEX WITH FLUORESCEIN Deposited 2002-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 16–189（174 aa）	Not recorded	FLU 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；298 K；2.0 M (NH4)2SO4, 2% (w/v) PEG 400, 10 mM hepes/naoh, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 298 KK	Resolution 2.00 Å R-free 0.243
1T0V NMR Solution Structure of the Engineered Lipocalin FluA(R95K) Northeast Structural Genomics Target OR17 Deposited 2004-04-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 16–189（174 aa）	Mutation：R95K	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.4；298 K；Ionic strength (raw mmCIF value) 150 mM NaCl; 10 mM Na-PO4; 50 mM benzamidine; 0.2 mM EDTA；Pressure ambient NMR sample composition 0.7 mM FluA(R95K) U-13C,15N 150 mM NaCl 10 mM Na-PO4 0.2 mM EDTA 50 mM benzamidine pH 6.4 \| 90% H2O/10% D2O NMR sample composition 0.7 mM FluA(R95K) U-50% 2H,15N 150 mM NaCl 10 mM Na-PO4 0.2 mM EDTA 50 mM benzamidine pH 6.4 \| 90% H2O/10% D2O NMR sample composition 0.7 mM FluA(R95K) U-15N 150 mM NaCl 10 mM Na-PO4 0.2 mM EDTA 50 mM benzamidine pH 6.4 \| 90% H2O/10% D2O NMR sample composition 0.7 mM FluA(R95K) 150 mM NaCl 10 mM Na-PO4 0.2 mM EDTA 50 mM benzamidine pH 6.4 \| 100% D2O NMR sample composition 0.7 mM FluA(R95K) 150 mM NaCl 10 mM Na-PO4 0.2 mM EDTA 50 mM benzamidine pH 6.4 \| 90% H2O/10% D2O	Resolution not provided

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BBP_PIEBR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–173； UniProt 16–188 Author chain B； PDBConstruct 1–173； UniProt 16–188 Author chain C； PDBConstruct 1–173； UniProt 16–188 Author chain D； PDBConstruct 1–173； UniProt 16–188

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	1bbp
Deposition date deposition_date	1990-09-19
Structure title title	MOLECULAR STRUCTURE OF THE BILIN BINDING PROTEIN (BBP) FROM PIERIS BRASSICAE AFTER REFINEMENT AT 2.0 ANGSTROMS RESOLUTION.
Keywords keywords	BILIN BINDING; BILIN BINDING
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	29.06 Å
Radius of gyration Rg (electron density) rg_electron	28.03 Å
Forward intensity I(0) i0	100945000.00
Molecular weight molecular_weight	80982.0 kDa
Excluded volume excluded_volume	101860 Å³
Envelope volume envelope_volume	126960 Å³
Hydration-shell volume shell_volume	37061 Å³
Envelope diameter envelope_diameter	95.5 Å
Shell Rg shell_rg	36.14 Å
Envelope Rg envelope_rg	27.69 Å
Shape Rg shape_rg	28.02 Å
Total Rg total_rg	28.91 Å
Total atoms total_atoms	5745
Residues n_residues	692
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	89.3 Å
Rg (real space) rg_real	28.92 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	1.0090e+08
I(0) uncertainty (real space) i0_real_error	1.4590e+06
Rg (reciprocal space) rg_reciprocal	28.98 Å
I(0) (reciprocal space) i0_reciprocal	100900000.0000
Solution quality estimate total_estimate	0.9058
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	39.0 Å
Skewness Skewness skewness	0.133
Kurtosis Kurtosis kurtosis	-0.514
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	27440000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.944; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.940

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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	BILIN BINDING PROTEIN
Molecular weight formula_weight	19703.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6169

NVYHDGACPEVKPVDNFDWSNYHGKWWEVAKYPNSVEKYGKCGWAEYTPEGKSVKVSNYHVIHGKEYFIEGTAYPVGDSKIGKIYHKLTYGGVTKENVFNVLSTDNKNYIIGYYCKYDEDKKGHQDFVWVLSRSKVLTGEAKTAVENYLIGSPVVDSQKLVYSDFSEAACKVN

来源 Source

来源生物 organism	Pieris brassicae
通用名 common_name	large cabbage white
NCBI Class编号 ncbi_taxonomy_id	7116

Entity 2 Entity 2 non-polymer

Description description	BILIVERDIN IX GAMMA CHROMOPHORE
Molecular weight formula_weight	582.6 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	424

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1bbpa_
Class class	b — All beta proteins
Fold Fold fold	b.60 — Lipocalins
Superfamily Superfamily superfamily	b.60.1 — Lipocalins
Family Family family	b.60.1.1 — Retinol binding protein-like

Domain ID domain_id	d1bbpb_
Class class	b — All beta proteins
Fold Fold fold	b.60 — Lipocalins
Superfamily Superfamily superfamily	b.60.1 — Lipocalins
Family Family family	b.60.1.1 — Retinol binding protein-like

Domain ID domain_id	d1bbpc_
Class class	b — All beta proteins
Fold Fold fold	b.60 — Lipocalins
Superfamily Superfamily superfamily	b.60.1 — Lipocalins
Family Family family	b.60.1.1 — Retinol binding protein-like

Domain ID domain_id	d1bbpd_
Class class	b — All beta proteins
Fold Fold fold	b.60 — Lipocalins
Superfamily Superfamily superfamily	b.60.1 — Lipocalins
Family Family family	b.60.1.1 — Retinol binding protein-like

CATH v4.4 (4 domains)

Domain ID domain_id	1bbpA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	20 — Calycin beta-barrel core domain

Domain ID domain_id	1bbpB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	20 — Calycin beta-barrel core domain

Domain ID domain_id	1bbpC00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	20 — Calycin beta-barrel core domain

Domain ID domain_id	1bbpD00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	20 — Calycin beta-barrel core domain

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8. Citations (2)

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Unit-cell length a length_a	132.100 Å
Unit-cell length b length_b	121.900 Å
Unit-cell length c length_c	63.800 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	16

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	0.2000
R_free r_free	—

fit	/app/data/saxs_computation/bb/1bbp/1bbp.fit
pddf	/app/data/pr_computation/bb/1bbp/1bbp.pr.out
profile	/app/data/saxs_computation/bb/1bbp/1bbp.dat

MOLECULAR STRUCTURE OF THE BILIN BINDING PROTEIN (BBP) FROM PIERIS BRASSICAE AFTER REFINEMENT AT 2.0 ANGSTROMS RESOLUTION.

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

BILIN BINDING PROTEIN

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