SAXSdb — 4dbb

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

Amyloid beta A4 precursor protein-binding family A member 1

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 453–496 Chain A； UniProt 509–643	Fragment：PTB DOMAIN, UNP residues 453-643 with deletion of residues 497-508	CL CHLORIDE ION × 1 ACY ACETIC ACID × 2 IPA ISOPROPYL ALCOHOL × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25% isopropanol, 25% glycerol, 0.1 M Hepes pH 7.5, 0.15 M NaCl, 0.2 M ammonium acetate, 2 mM TCEP, vapor diffusion, hanging drop, temperature 293K	Resolution 1.90 Å R-free 0.225

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 4DBB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6KMH The crystal structure of CASK/Mint1 complex Deposited 2019-07-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 338–397（60 aa）	Not recorded	IOD IODIDE ION × 7 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2M KI, 20% PEG 3350, pH 7.0	Resolution 2.40 Å R-free 0.224
6KMH The crystal structure of CASK/Mint1 complex Deposited 2019-07-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 338–397（60 aa）	Not recorded	IOD IODIDE ION × 5 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2M KI, 20% PEG 3350, pH 7.0	Resolution 2.40 Å R-free 0.224
7XSJ The structure of the Mint1/Munc18-1/syntaxin-1 complex Deposited 2022-05-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 227–303（77 aa） Fragment：MID	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；297 K；0.2M Sodium Malonate, pH 7.0, 20% (v/v) PEG 3350	Resolution 3.20 Å R-free 0.270
9M6G the crystal structure of the Ca2+/CaM-CASK-CaMK-Mint1-CID complex Deposited 2025-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 338–397（60 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MLI MALONATE ION × 1 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；289 K；0.1 M Sodium malonate, pH 5.0, 12% (v/v) PEG 3350	Resolution 1.70 Å R-free 0.187

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

View Construct and Data Evidence

UniProt name	APBA1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–44； UniProt 453–496 Author chain A； PDBConstruct 45–162； UniProt 509–643

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	4dbb
Deposition date deposition_date	2012-01-13
Structure title title	The PTB domain of Mint1 is autoinhibited by a helix in the C-terminal linker region
Keywords keywords	X11S/MINTS, PTB DOMAIN, CHIMERA PROTEIN, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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	17.42 Å
Radius of gyration Rg (electron density) rg_electron	16.14 Å
Forward intensity I(0) i0	6096020.00
Molecular weight molecular_weight	17539.0 kDa
Excluded volume excluded_volume	21925 Å³
Envelope volume envelope_volume	27063 Å³
Hydration-shell volume shell_volume	14389 Å³
Envelope diameter envelope_diameter	54.6 Å
Shell Rg shell_rg	21.70 Å
Envelope Rg envelope_rg	16.48 Å
Shape Rg shape_rg	16.14 Å
Total Rg total_rg	17.19 Å
Total atoms total_atoms	2463
Residues n_residues	150
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	55.7 Å
Rg (real space) rg_real	17.33 Å
Rg uncertainty (real space) rg_real_error	0.31 Å
I(0) (real space) i0_real	6.0960e+06
I(0) uncertainty (real space) i0_real_error	6.6740e+04
Rg (reciprocal space) rg_reciprocal	17.35 Å
I(0) (reciprocal space) i0_reciprocal	6096000.0000
Solution quality estimate total_estimate	0.8954
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.3 Å
Skewness Skewness skewness	0.184
Kurtosis Kurtosis kurtosis	-0.354
Angular range angular_range	— – 0.4550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	976200.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.881; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.992

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Amyloid beta A4 precursor protein-binding family A member 1
Molecular weight formula_weight	18408.9 kDa
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	2558

DPEDLIDGIIFAANYLGSTQLLSDKTPSKNVRMMQAQEAVSRIKPEGESQPMTEVDLFISTQRIKVLNADTQEPMMDHPLRTISYIADIGNIVVLMARRRMPRSQYKMICHVFESEDAQLIAQSIGQAFSVAYQEFLRANGINPEDLSQKEYSDLLNTQDMY

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ISOPROPYL ALCOHOL
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	78

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4dbba_
Class class	b — All beta proteins
Fold Fold fold	b.55 — PH domain-like barrel
Superfamily Superfamily superfamily	b.55.1 — PH domain-like
Family Family family	b.55.1.2 — Phosphotyrosine-binding domain (PTB)

CATH v4.4 (1 domains)

Domain ID domain_id	4dbbA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	29 — PH-domain like
Homologous superfamily homologous superfamily	30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)

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8. Citations (1)

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Unit-cell length a length_a	64.729 Å
Unit-cell length b length_b	64.729 Å
Unit-cell length c length_c	115.155 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	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.901 Å
Low-resolution limit resolution_low	33.016 Å
R factor r_factor	0.1980
R_work r_work	0.1966
R_free r_free	0.2252

fit	/app/data/saxs_computation/db/4dbb/4dbb.fit
pddf	/app/data/pr_computation/db/4dbb/4dbb.pr.out
profile	/app/data/saxs_computation/db/4dbb/4dbb.dat

The PTB domain of Mint1 is autoinhibited by a helix in the C-terminal linker region