SAXSdb — 1dk5

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

ANNEXIN 24(CA32)

Capsicum annuum

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 1–314	Not recorded	SO4 SULFATE ION × 14	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；288 K；1.7 M (NH4)2SO4, 2 mM CaCl2, 0.1 M NaAc , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 15K	Resolution 2.80 Å R-free 0.316
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–314	Not recorded	SO4 SULFATE ION × 19	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；288 K；1.7 M (NH4)2SO4, 2 mM CaCl2, 0.1 M NaAc , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 15K	Resolution 2.80 Å R-free 0.316
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–314 Chain B； UniProt 1–314	Not recorded	SO4 SULFATE ION × 33	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；288 K；1.7 M (NH4)2SO4, 2 mM CaCl2, 0.1 M NaAc , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 15K	Resolution 2.80 Å R-free 0.316
4	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–314 Chain B； UniProt 1–314	Not recorded	SO4 SULFATE ION × 33	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；288 K；1.7 M (NH4)2SO4, 2 mM CaCl2, 0.1 M NaAc , pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 15K	Resolution 2.80 Å R-free 0.316

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	Q42657_CAPAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 9–322； UniProt 1–314 Author chain B； PDBConstruct 9–322； UniProt 1–314

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	1dk5
Deposition date deposition_date	1999-12-06
Structure title title	CRYSTAL STRUCTURE OF ANNEXIN 24(CA32) FROM CAPSICUM ANNUUM
Keywords keywords	PLANT ANNEXIN, CAPSICUM ANNUUM, BELL PEPPER, CALCIUM BINDING PROTEIN, 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	50.54 Å
Radius of gyration Rg (electron density) rg_electron	50.62 Å
Forward intensity I(0) i0	93517800.00
Molecular weight molecular_weight	75147.0 kDa
Excluded volume excluded_volume	91924 Å³
Envelope volume envelope_volume	149220 Å³
Hydration-shell volume shell_volume	24353 Å³
Envelope diameter envelope_diameter	153.2 Å
Shell Rg shell_rg	56.67 Å
Envelope Rg envelope_rg	47.63 Å
Shape Rg shape_rg	50.63 Å
Total Rg total_rg	50.81 Å
Total atoms total_atoms	5244
Residues n_residues	630
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	142.6 Å
Rg (real space) rg_real	50.94 Å
Rg uncertainty (real space) rg_real_error	1.40 Å
I(0) (real space) i0_real	9.3520e+07
I(0) uncertainty (real space) i0_real_error	1.9460e+06
Rg (reciprocal space) rg_reciprocal	50.16 Å
I(0) (reciprocal space) i0_reciprocal	93420000.0000
Solution quality estimate total_estimate	0.5468
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.6 Å
Skewness Skewness skewness	0.177
Kurtosis Kurtosis kurtosis	-1.427
Angular range angular_range	— – 0.1550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3464000.0000
Real-space data points n_real_points	32
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.024; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.032; 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	ANNEXIN 24(CA32)
Molecular weight formula_weight	36940.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5572

MAHHHHHHMASLTVPAHVPSAAEDCEQLRSAFKGWGTNEKLIISILAHRTAAQRKLIRQTYAETFGEDLLKELDRELTHDFEKLVLVWTLDPSERDAHLAKEATKRWTKSNFVLVELACTRSPKELVLAREAYHARYKKSLEEDVAYHTTGDHRKLLVPLVSSYRYGGEEVDLRLAKAESKILHEKISDKAYSDDEVIRILATRSKAQLNATLNHYKDEHGEDILKQLEDGDEFVALLRATIKGLVYPEHYFVEVLRDAINRRGTEEDHLTRVIATRAEVDLKIIADEYQKRDSIPLGRAIAKDTRGDYESMLLALLGQEED

来源 Source

来源生物 organism	Capsicum annuum
NCBI Class编号 ncbi_taxonomy_id	4072
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	33

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	328

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1dk5a1
Class class	a — All alpha proteins
Fold Fold fold	a.65 — Annexin
Superfamily Superfamily superfamily	a.65.1 — Annexin
Family Family family	a.65.1.1 — Annexin

Domain ID domain_id	d1dk5a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1dk5b1
Class class	a — All alpha proteins
Fold Fold fold	a.65 — Annexin
Superfamily Superfamily superfamily	a.65.1 — Annexin
Family Family family	a.65.1.1 — Annexin

Domain ID domain_id	d1dk5b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (8 domains)

Domain ID domain_id	1dk5A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

Domain ID domain_id	1dk5A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

Domain ID domain_id	1dk5A03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

Domain ID domain_id	1dk5A04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

Domain ID domain_id	1dk5B01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

Domain ID domain_id	1dk5B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

Domain ID domain_id	1dk5B03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

Domain ID domain_id	1dk5B04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

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8. Citations (2)

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Unit-cell length a length_a	96.760 Å
Unit-cell length b length_b	96.760 Å
Unit-cell length c length_c	173.390 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	12

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2160
R_work r_work	0.2160
R_free r_free	0.3160

fit	/app/data/saxs_computation/dk/1dk5/1dk5.fit
pddf	/app/data/pr_computation/dk/1dk5/1dk5.pr.out
profile	/app/data/saxs_computation/dk/1dk5/1dk5.dat

CRYSTAL STRUCTURE OF ANNEXIN 24(CA32) FROM CAPSICUM ANNUUM

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

ANNEXIN 24(CA32)

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