1bb9

CRYSTAL STRUCTURE OF THE SH3 DOMAIN FROM RAT AMPHIPHYSIN 2

Method: X-RAY DIFFRACTION D_max: 43.6 Å Quality: GOOD

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

AMPHIPHYSIN 2

Rattus norvegicus

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 495–588	Fragment：SH3 DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；VAPOUR DIFFUSION, PROTEIN 30MG/ML, RESERVOIR 2.0M AMMONIUM SULFATE, 100MM NA CITRATE PH6.0, PLUS 2MM DTT., vapor diffusion	Resolution 2.20 Å R-free 0.264

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	BIN1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–115； UniProt 495–588

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1bb9
Deposition date deposition_date	1998-04-29
Structure title title	CRYSTAL STRUCTURE OF THE SH3 DOMAIN FROM RAT AMPHIPHYSIN 2
Keywords keywords	TRANSFERASE, SH3 DOMAIN; TRANSFERASE
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	13.66 Å
Radius of gyration Rg (electron density) rg_electron	12.14 Å
Forward intensity I(0) i0	1996660.00
Molecular weight molecular_weight	9366.0 kDa
Excluded volume excluded_volume	11622 Å³
Envelope volume envelope_volume	13281 Å³
Hydration-shell volume shell_volume	9518 Å³
Envelope diameter envelope_diameter	42.1 Å
Shell Rg shell_rg	17.52 Å
Envelope Rg envelope_rg	12.45 Å
Shape Rg shape_rg	12.14 Å
Total Rg total_rg	13.49 Å
Total atoms total_atoms	661
Residues n_residues	83
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	43.6 Å
Rg (real space) rg_real	13.56 Å
Rg uncertainty (real space) rg_real_error	0.23 Å
I(0) (real space) i0_real	1.9970e+06
I(0) uncertainty (real space) i0_real_error	1.9670e+04
Rg (reciprocal space) rg_reciprocal	13.57 Å
I(0) (reciprocal space) i0_reciprocal	1997000.0000
Solution quality estimate total_estimate	0.8876
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	42.5 Å
Skewness Skewness skewness	0.082
Kurtosis Kurtosis kurtosis	-0.373
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	393400.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.850; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; 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	d1bb9a_
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.2 — SH3-domain
Family Family family	b.34.2.1 — SH3-domain

CATH v4.4 (1 domains)

Domain ID domain_id	1bb9A00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

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8. Citations (1)

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Unit-cell length a length_a	72.140 Å
Unit-cell length b length_b	72.140 Å
Unit-cell length c length_c	34.560 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	36.000 Å
R factor r_factor	—
R_work r_work	0.1860
R_free r_free	0.2640

Description description	AMPHIPHYSIN 2
Molecular weight formula_weight	12879.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	745

CRYSTAL STRUCTURE OF THE SH3 DOMAIN FROM RAT AMPHIPHYSIN 2

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

AMPHIPHYSIN 2

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) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
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	60

fit	/app/data/saxs_computation/bb/1bb9/1bb9.fit
pddf	/app/data/pr_computation/bb/1bb9/1bb9.pr.out
profile	/app/data/saxs_computation/bb/1bb9/1bb9.dat