SAXSdb — 1bp1

▼

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

BACTERICIDAL/PERMEABILITY-INCREASING PROTEIN

Homo sapiens

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 28–483	Mutation：S351A	PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.8；CRYSTALLIZED IN 12% PEG 8000, 0.2 M MG ACETATE, 0.1 NA CACODYLATE PH 6.8	Resolution 2.40 Å R-free 0.295

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 1BP1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EWF THE 1.7 ANGSTROM CRYSTAL STRUCTURE OF BPI Deposited 2000-04-25	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–483（456 aa）	Mutation：S351A	PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；289 K；12 % PEG 6000, 0.2 M Mg Acetate, 0.1 M Na Cacodylate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 16K	Resolution 1.70 Å R-free 0.250

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	BPI_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–456； UniProt 28–483

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1bp1
Deposition date deposition_date	1997-04-08
Structure title title	CRYSTAL STRUCTURE OF BPI, THE HUMAN BACTERICIDAL PERMEABILITY-INCREASING PROTEIN
Keywords keywords	BACTERICIDAL, PERMEABILITY-INCREASING, LIPID-BINDING, LIPOPOLYSACCHARIDE-BINDING, ANTIBIOTIC; BACTERICIDAL
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	34.37 Å
Radius of gyration Rg (electron density) rg_electron	35.32 Å
Forward intensity I(0) i0	37323100.00
Molecular weight molecular_weight	51576.0 kDa
Excluded volume excluded_volume	66033 Å³
Envelope volume envelope_volume	84495 Å³
Hydration-shell volume shell_volume	24054 Å³
Envelope diameter envelope_diameter	138.2 Å
Shell Rg shell_rg	33.95 Å
Envelope Rg envelope_rg	36.46 Å
Shape Rg shape_rg	35.36 Å
Total Rg total_rg	35.04 Å
Total atoms total_atoms	3629
Residues n_residues	456
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	132.1 Å
Rg (real space) rg_real	35.10 Å
Rg uncertainty (real space) rg_real_error	2.03 Å
I(0) (real space) i0_real	3.7320e+07
I(0) uncertainty (real space) i0_real_error	8.2570e+05
Rg (reciprocal space) rg_reciprocal	34.64 Å
I(0) (reciprocal space) i0_reciprocal	37310000.0000
Solution quality estimate total_estimate	0.6617
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	23.0 Å
Skewness Skewness skewness	0.751
Kurtosis Kurtosis kurtosis	-0.067
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10770000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.212; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.101; Smooth: 0.860

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	BACTERICIDAL/PERMEABILITY-INCREASING PROTEIN
Molecular weight formula_weight	50703.7 kDa
Mutation mutation	S351A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3677

VNPGVVVRISQKGLDYASQQGTAALQKELKRIKIPDYSDSFKIKHLGKGHYSFYSMDIREFQLPSSQISMVPNVGLKFSISNANIKISGKWKAQKRFLKMSGNFDLSIEGMSISADLKLGSNPTSGKPTITCSSCSSHINSVHVHISKSKVGWLIQLFHKKIESALRNKMNSQVCEKVTNSVSSKLQPYFQTLPVMTKIDSVAGINYGLVAPPATTAETLDVQMKGEFYSENHHNPPPFAPPVMEFPAAHDRMVYLGLSDYFFNTAGLVYQEAGVLKMTLRDDMIPKESKFRLTTKFFGTFLPEVAKKFPNMKIQIHVSASTPPHLSVQPTGLTFYPAVDVQAFAVLPNSALASLFLIGMHTTGSMEVSAESNRLVGELKLDRLLLELKHSNIGPFPVELLQDIMNYIVPILVLPRVNEKLQKGFPLPTPARVQLYNVVLQPHQNFLLFGADVVYK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cricetulus griseus

Entity 2 Entity 2 non-polymer

Description description	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Molecular weight formula_weight	790.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	48

▼

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1bp1a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.83 — Aha1/BPI domain-like
Superfamily Superfamily superfamily	d.83.1 — Bactericidal permeability-increasing protein, BPI
Family Family family	d.83.1.1 — Bactericidal permeability-increasing protein, BPI

Domain ID domain_id	d1bp1a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.83 — Aha1/BPI domain-like
Superfamily Superfamily superfamily	d.83.1 — Bactericidal permeability-increasing protein, BPI
Family Family family	d.83.1.1 — Bactericidal permeability-increasing protein, BPI

CATH v4.4 (2 domains)

Domain ID domain_id	1bp1A01
Class class	3 — Alpha Beta
Architecture architecture	15 — Super Roll
Topology topology	10 — Bactericidal permeability-increasing protein; domain 1
Homologous superfamily homologous superfamily	10 — Bactericidal permeability-increasing protein; domain 1

Domain ID domain_id	1bp1A02
Class class	3 — Alpha Beta
Architecture architecture	15 — Super Roll
Topology topology	20 — Bactericidal permeability-increasing protein; domain 2
Homologous superfamily homologous superfamily	10 — Bactericidal permeability-increasing protein; domain 2

▶

8. Citations (2)

▶

Unit-cell length a length_a	185.600 Å
Unit-cell length b length_b	33.000 Å
Unit-cell length c length_c	85.200 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.60 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2250
R_work r_work	0.2250
R_free r_free	0.2950

fit	/app/data/saxs_computation/bp/1bp1/1bp1.fit
pddf	/app/data/pr_computation/bp/1bp1/1bp1.pr.out
profile	/app/data/saxs_computation/bp/1bp1/1bp1.dat

CRYSTAL STRUCTURE OF BPI, THE HUMAN BACTERICIDAL PERMEABILITY-INCREASING PROTEIN

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

BACTERICIDAL/PERMEABILITY-INCREASING 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

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