1d0n

THE CRYSTAL STRUCTURE OF CALCIUM-FREE EQUINE PLASMA GELSOLIN.

Method: X-RAY DIFFRACTION D_max: 180.7 Å Quality: REASONABLE

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

HORSE PLASMA GELSOLIN

OrganismNot specified

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 2–730 Chain B； UniProt 2–730	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；ammonium sulfate, Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 18K	Resolution 2.50 Å R-free 0.238
2	Protein homooligomer Homooligomer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 2–730 Chain B； UniProt 2–730	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；ammonium sulfate, Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 18K	Resolution 2.50 Å R-free 0.238

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 1D0N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1RGI Crystal structure of gelsolin domains G1-G3 bound to actin Deposited 2003-11-12	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 G 1–346（346 aa） Fragment：domains G1-G3	Not recorded	CA CALCIUM ION × 4 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；277 K；2% PEG 8000, 100 mM Sodium acetate, 1 mM CaCl2, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.00 Å R-free 0.258
2FGH ATP bound gelsolin Deposited 2005-12-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–730（730 aa） Chain B 1–730（730 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；crystals were grown from drops containing a 1:1 ratio of 34% saturated ammonium sulfate solution, 100mM Tris-HCL reservoir solution, pH 8.0, VAPOR DIFFUSION	Resolution 2.80 Å R-free 0.265
2FGH ATP bound gelsolin Deposited 2005-12-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–730（730 aa） Chain B 1–730（730 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；crystals were grown from drops containing a 1:1 ratio of 34% saturated ammonium sulfate solution, 100mM Tris-HCL reservoir solution, pH 8.0, VAPOR DIFFUSION	Resolution 2.80 Å R-free 0.265

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

View Construct and Data Evidence

UniProt name	GELS_HORSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–729； UniProt 2–730 Author chain B； PDBConstruct 1–729； UniProt 2–730

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	1d0n
Deposition date deposition_date	1999-09-13
Structure title title	THE CRYSTAL STRUCTURE OF CALCIUM-FREE EQUINE PLASMA GELSOLIN.
Keywords keywords	MIXED ALPHA-BETA STRUCTURE, ACTIN-BINDING PROTEIN, PROTEIN DOMAIN PACKING, CONTRACTILE PROTEIN; CONTRACTILE 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	48.29 Å
Radius of gyration Rg (electron density) rg_electron	49.20 Å
Forward intensity I(0) i0	387963000.00
Molecular weight molecular_weight	161170.0 kDa
Excluded volume excluded_volume	201050 Å³
Envelope volume envelope_volume	278960 Å³
Hydration-shell volume shell_volume	52095 Å³
Envelope diameter envelope_diameter	180.2 Å
Shell Rg shell_rg	46.69 Å
Envelope Rg envelope_rg	49.25 Å
Shape Rg shape_rg	49.19 Å
Total Rg total_rg	49.11 Å
Total atoms total_atoms	11382
Residues n_residues	1458
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	180.7 Å
Rg (real space) rg_real	49.24 Å
Rg uncertainty (real space) rg_real_error	2.69 Å
I(0) (real space) i0_real	3.8800e+08
I(0) uncertainty (real space) i0_real_error	7.6070e+06
Rg (reciprocal space) rg_reciprocal	48.30 Å
I(0) (reciprocal space) i0_reciprocal	387500000.0000
Solution quality estimate total_estimate	0.7097
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	38.3 Å
Skewness Skewness skewness	0.622
Kurtosis Kurtosis kurtosis	-0.365
Angular range angular_range	— – 0.1650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	51440000.0000
Real-space data points n_real_points	34
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.354; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.394; Smooth: 0.766

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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) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1d0na1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.109 — Gelsolin-like
Superfamily Superfamily superfamily	d.109.1 — Actin depolymerizing proteins
Family Family family	d.109.1.1 — Gelsolin-like

Domain ID domain_id	d1d0na2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.109 — Gelsolin-like
Superfamily Superfamily superfamily	d.109.1 — Actin depolymerizing proteins
Family Family family	d.109.1.1 — Gelsolin-like

Domain ID domain_id	d1d0na3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.109 — Gelsolin-like
Superfamily Superfamily superfamily	d.109.1 — Actin depolymerizing proteins
Family Family family	d.109.1.1 — Gelsolin-like

Domain ID domain_id	d1d0na4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.109 — Gelsolin-like
Superfamily Superfamily superfamily	d.109.1 — Actin depolymerizing proteins
Family Family family	d.109.1.1 — Gelsolin-like

Domain ID domain_id	d1d0na5
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.109 — Gelsolin-like
Superfamily Superfamily superfamily	d.109.1 — Actin depolymerizing proteins
Family Family family	d.109.1.1 — Gelsolin-like

Domain ID domain_id	d1d0na6
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.109 — Gelsolin-like
Superfamily Superfamily superfamily	d.109.1 — Actin depolymerizing proteins
Family Family family	d.109.1.1 — Gelsolin-like

Domain ID domain_id	d1d0nb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.109 — Gelsolin-like
Superfamily Superfamily superfamily	d.109.1 — Actin depolymerizing proteins
Family Family family	d.109.1.1 — Gelsolin-like

Domain ID domain_id	d1d0nb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.109 — Gelsolin-like
Superfamily Superfamily superfamily	d.109.1 — Actin depolymerizing proteins
Family Family family	d.109.1.1 — Gelsolin-like

Domain ID domain_id	d1d0nb3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.109 — Gelsolin-like
Superfamily Superfamily superfamily	d.109.1 — Actin depolymerizing proteins
Family Family family	d.109.1.1 — Gelsolin-like

Domain ID domain_id	d1d0nb4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.109 — Gelsolin-like
Superfamily Superfamily superfamily	d.109.1 — Actin depolymerizing proteins
Family Family family	d.109.1.1 — Gelsolin-like

Domain ID domain_id	d1d0nb5
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.109 — Gelsolin-like
Superfamily Superfamily superfamily	d.109.1 — Actin depolymerizing proteins
Family Family family	d.109.1.1 — Gelsolin-like

Domain ID domain_id	d1d0nb6
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.109 — Gelsolin-like
Superfamily Superfamily superfamily	d.109.1 — Actin depolymerizing proteins
Family Family family	d.109.1.1 — Gelsolin-like

CATH v4.4 (12 domains)

Domain ID domain_id	1d0nA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	20 — Severin
Homologous superfamily homologous superfamily	10 — Severin

Domain ID domain_id	1d0nA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	20 — Severin
Homologous superfamily homologous superfamily	10 — Severin

Domain ID domain_id	1d0nA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	20 — Severin
Homologous superfamily homologous superfamily	10 — Severin

Domain ID domain_id	1d0nA04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	20 — Severin
Homologous superfamily homologous superfamily	10 — Severin

Domain ID domain_id	1d0nA05
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	20 — Severin
Homologous superfamily homologous superfamily	10 — Severin

Domain ID domain_id	1d0nA06
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	20 — Severin
Homologous superfamily homologous superfamily	10 — Severin

Domain ID domain_id	1d0nB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	20 — Severin
Homologous superfamily homologous superfamily	10 — Severin

Domain ID domain_id	1d0nB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	20 — Severin
Homologous superfamily homologous superfamily	10 — Severin

Domain ID domain_id	1d0nB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	20 — Severin
Homologous superfamily homologous superfamily	10 — Severin

Domain ID domain_id	1d0nB04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	20 — Severin
Homologous superfamily homologous superfamily	10 — Severin

Domain ID domain_id	1d0nB05
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	20 — Severin
Homologous superfamily homologous superfamily	10 — Severin

Domain ID domain_id	1d0nB06
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	20 — Severin
Homologous superfamily homologous superfamily	10 — Severin

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8. Citations (1)

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Unit-cell length a length_a	169.400 Å
Unit-cell length b length_b	169.400 Å
Unit-cell length c length_c	154.200 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	16

Space group space_group	P 4 21 2
Space-group number int_tables_number	90
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2116
R_work r_work	0.2049
R_free r_free	0.2376

Description description	HORSE PLASMA GELSOLIN
Molecular weight formula_weight	80691.5 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	11666

THE CRYSTAL STRUCTURE OF CALCIUM-FREE EQUINE PLASMA GELSOLIN.

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

HORSE PLASMA GELSOLIN

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

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

CATH v4.4 (12 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	284

fit	/app/data/saxs_computation/d0/1d0n/1d0n.fit
pddf	/app/data/pr_computation/d0/1d0n/1d0n.pr.out
profile	/app/data/saxs_computation/d0/1d0n/1d0n.dat