SAXSdb — 1bd9

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

PHOSPHATIDYLETHANOLAMINE BINDING 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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–186 Chain B； UniProt 1–186	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；PROTEIN WAS CRYSTALLIZED FROM 28-32% PEG 4000/6000/8000, 200-300 MM SODIUM ACETATE, 100MM SODIUM CACODYLATE, PH 6.5; THEN SOAKED IN 28-32% PEG 4000/6000/8000, 200-300 MM SODIUM ACETATE, 100MM BIS-TRIS, PH 6.5.	Resolution 2.05 Å R-free 0.232

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 1BD9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BEH HUMAN PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN IN COMPLEX WITH CACODYLATE Deposited 1998-05-14	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 1–186（186 aa）	Not recorded	CAC CACODYLATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PROTEIN WAS CRYSTALLIZED FROM 28-32% PEG 4000/6000/8000, 200-300 MM SODIUM ACETATE, 100MM SODIUM CACODYLATE., pH 6.5	Resolution 1.75 Å R-free 0.286
1BEH HUMAN PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN IN COMPLEX WITH CACODYLATE Deposited 1998-05-14	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 1–186（186 aa）	Not recorded	CAC CACODYLATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PROTEIN WAS CRYSTALLIZED FROM 28-32% PEG 4000/6000/8000, 200-300 MM SODIUM ACETATE, 100MM SODIUM CACODYLATE., pH 6.5	Resolution 1.75 Å R-free 0.286
2L7W Solution structure of the human Raf-1 kinase inhibitor protein Deposited 2010-12-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–187（187 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4；298 K；Ionic strength (raw mmCIF value) 200 NMR sample composition 3mM [U-100% 13C; U-100% 15N] Raf-1 kinase inhibitor protein; 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2QYQ Human raf kinase inhibitor protein (rkip) in complex with o-phosphotyrosine Deposited 2007-08-15	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 1–187（187 aa）	Not recorded	PTR O-PHOSPHOTYROSINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；Initial crystallisation: 32-34% PEG 4OOO or 8000, 0.2 M sodium acetate, 0.1 M sodium acetate pH 4.0. Complex formed by soaking in: 32% PEG 4OOO, 0.2 M sodium chloride, 0.1 M O-phosphotyrosine, 0.1 M hepes pH 7.0., VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.95 Å R-free 0.208

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PEBP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–187； UniProt 1–186 Author chain B； PDBConstruct 2–187； UniProt 1–186

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	1bd9
Deposition date deposition_date	1998-05-12
Structure title title	HUMAN PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN
Keywords keywords	LIPID-BINDING, SIGNALLING, LIPID BINDING PROTEIN; LIPID BINDING PROTEIN
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	23.13 Å
Radius of gyration Rg (electron density) rg_electron	22.33 Å
Forward intensity I(0) i0	28466600.00
Molecular weight molecular_weight	41104.0 kDa
Excluded volume excluded_volume	51477 Å³
Envelope volume envelope_volume	59839 Å³
Hydration-shell volume shell_volume	22789 Å³
Envelope diameter envelope_diameter	76.4 Å
Shell Rg shell_rg	28.53 Å
Envelope Rg envelope_rg	22.37 Å
Shape Rg shape_rg	22.31 Å
Total Rg total_rg	23.15 Å
Total atoms total_atoms	2908
Residues n_residues	365
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	76.4 Å
Rg (real space) rg_real	23.14 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	2.8470e+07
I(0) uncertainty (real space) i0_real_error	4.2170e+05
Rg (reciprocal space) rg_reciprocal	23.14 Å
I(0) (reciprocal space) i0_reciprocal	28470000.0000
Solution quality estimate total_estimate	0.8836
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.7 Å
Skewness Skewness skewness	0.351
Kurtosis Kurtosis kurtosis	-0.467
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8122000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.980

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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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1bd9a_
Class class	b — All beta proteins
Fold Fold fold	b.17 — PEBP-like
Superfamily Superfamily superfamily	b.17.1 — PEBP-like
Family Family family	b.17.1.1 — Phosphatidylethanolamine binding protein

Domain ID domain_id	d1bd9b_
Class class	b — All beta proteins
Fold Fold fold	b.17 — PEBP-like
Superfamily Superfamily superfamily	b.17.1 — PEBP-like
Family Family family	b.17.1.1 — Phosphatidylethanolamine binding protein

CATH v4.4 (2 domains)

Domain ID domain_id	1bd9A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	280 — Phosphatidylethanolamine-binding Protein
Homologous superfamily homologous superfamily	10 — PEBP-like

Domain ID domain_id	1bd9B00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	280 — Phosphatidylethanolamine-binding Protein
Homologous superfamily homologous superfamily	10 — PEBP-like

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8. Citations (1)

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Unit-cell length a length_a	45.420 Å
Unit-cell length b length_b	60.740 Å
Unit-cell length c length_c	67.640 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.42 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1710
R_free r_free	0.2320

Description description	PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN
Molecular weight formula_weight	21086.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3302

HUMAN PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN

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

PHOSPHATIDYLETHANOLAMINE 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

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

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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	Escherichia coli BL21

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	394

fit	/app/data/saxs_computation/bd/1bd9/1bd9.fit
pddf	/app/data/pr_computation/bd/1bd9/1bd9.pr.out
profile	/app/data/saxs_computation/bd/1bd9/1bd9.dat