SAXSdb — 1dcq

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

PYK2-ASSOCIATED PROTEIN BETA

Mus musculus

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 421–697	Fragment：ARF-GAP DOMAIN	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 9.5；PEG 4000, 0.2 M sodium acetate, 0.1 M Tris-HCl (pH 9.5), 15% ethylene glycol, VAPOR DIFFUSION, HANGING DROP	Resolution 2.10 Å R-free 0.266

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	DDEF2_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–278； UniProt 421–697

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	1dcq
Deposition date deposition_date	1999-11-05
Structure title title	CRYSTAL STRUCTURE OF THE ARF-GAP DOMAIN AND ANKYRIN REPEATS OF PAPBETA.
Keywords keywords	ZINC-BINDING MODULE, ANKYRIN REPEATS, METAL BINDING PROTEIN; METAL 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	19.96 Å
Radius of gyration Rg (electron density) rg_electron	18.98 Å
Forward intensity I(0) i0	16407300.00
Molecular weight molecular_weight	29691.0 kDa
Excluded volume excluded_volume	36775 Å³
Envelope volume envelope_volume	41818 Å³
Hydration-shell volume shell_volume	18717 Å³
Envelope diameter envelope_diameter	68.0 Å
Shell Rg shell_rg	24.99 Å
Envelope Rg envelope_rg	19.17 Å
Shape Rg shape_rg	18.98 Å
Total Rg total_rg	19.80 Å
Total atoms total_atoms	2074
Residues n_residues	276
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	67.4 Å
Rg (real space) rg_real	19.91 Å
Rg uncertainty (real space) rg_real_error	0.44 Å
I(0) (real space) i0_real	1.6410e+07
I(0) uncertainty (real space) i0_real_error	2.0010e+05
Rg (reciprocal space) rg_reciprocal	19.92 Å
I(0) (reciprocal space) i0_reciprocal	16410000.0000
Solution quality estimate total_estimate	0.8055
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.8 Å
Skewness Skewness skewness	0.292
Kurtosis Kurtosis kurtosis	-0.350
Angular range angular_range	— – 0.4000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3630000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.832; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.000

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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	PYK2-ASSOCIATED PROTEIN BETA
Molecular weight formula_weight	30889.3 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	2169

MELTKEIISEVQRMTGNDVCCDCGAPDPTWLSTNLGILTCIECSGIHRELGVHYSRMQSLTLDVLGTSELLLAKNIGNAGFNEIMECCLPSEDPVKPNPGSDMIARKDYITAKYMERRYARKKHADTAAKLHSLCEAVKTRDIFGLLQAYADGVDLTEKIPLANGHEPDETALHLAVRSVDRTSLHIVDFLVQNSGNLDKQTGKGSTALHYCCLTDNAECLKLLLRGKASIEIANESGETPLDIAKRLKHEHCEELLTQALSGRFNSHVHVEYEWRLL

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	95

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1dcqa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.211 — beta-hairpin-alpha-hairpin repeat
Superfamily Superfamily superfamily	d.211.1 — Ankyrin repeat
Family Family family	d.211.1.1 — Ankyrin repeat

Domain ID domain_id	d1dcqa2
Class class	g — Small proteins
Fold Fold fold	g.45 — ArfGap/RecO-like zinc finger
Superfamily Superfamily superfamily	g.45.1 — ArfGap/RecO-like zinc finger
Family Family family	g.45.1.1 — Pyk2-associated protein beta ARF-GAP domain

CATH v4.4 (2 domains)

Domain ID domain_id	1dcqA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	150 — Arf GTPase activating protein

Domain ID domain_id	1dcqA02
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	20 — Ankyrin repeat-containing domain

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8. Citations (2)

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Unit-cell length a length_a	73.935 Å
Unit-cell length b length_b	132.208 Å
Unit-cell length c length_c	59.817 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.2300
R_work r_work	0.2130
R_free r_free	0.2660

fit	/app/data/saxs_computation/dc/1dcq/1dcq.fit
pddf	/app/data/pr_computation/dc/1dcq/1dcq.pr.out
profile	/app/data/saxs_computation/dc/1dcq/1dcq.dat

CRYSTAL STRUCTURE OF THE ARF-GAP DOMAIN AND ANKYRIN REPEATS OF PAPBETA.

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

PYK2-ASSOCIATED PROTEIN BETA

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