SAXSdb — 1vdi

▼

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

Troponin I, fast skeletal muscle

Gallus gallus

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 131–182	Fragment：residues 131-182	No other associated polymer	SOLUTION NMR mmCIF provides none of the parsed experimental conditions	Resolution not provided

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 1VDI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1VDJ Solution structure of actin-binding domain of troponin in Ca2+-bound state Deposited 2004-03-22	Parsed fields agree	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 131–182（52 aa） Fragment：residues 131-182	Not recorded	No recorded non-water small molecule	SOLUTION NMR mmCIF provides none of the parsed conditions	Resolution not provided
1YTZ Crystal structure of skeletal muscle troponin in the Ca2+-activated state Deposited 2005-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 1–182（182 aa）	Not recorded	DR6 ALPHA-[4-(1,1,3,3 - TETRAMETHYLBUTYL)PHENYL]-OMEGA-HYDROXY-POLY(OXY-1,2-ETHANEDIYL) × 3 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；0.4 M NaH2PO4/1.6 M K2HPO4, 200 mM NaCl, 0.1 M immidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.00 Å R-free 0.338
1YTZ Crystal structure of skeletal muscle troponin in the Ca2+-activated state Deposited 2005-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain I 1–182（182 aa）	Not recorded	DR6 ALPHA-[4-(1,1,3,3 - TETRAMETHYLBUTYL)PHENYL]-OMEGA-HYDROXY-POLY(OXY-1,2-ETHANEDIYL) × 6 CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；0.4 M NaH2PO4/1.6 M K2HPO4, 200 mM NaCl, 0.1 M immidazole, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.00 Å R-free 0.338
1YV0 Crystal structure of skeletal muscle troponin in the Ca2+-free state Deposited 2005-02-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 1–137（137 aa）	Not recorded	MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1.6 M tri-Sodium Citrate dihydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 7.00 Å R-free 0.359
1YV0 Crystal structure of skeletal muscle troponin in the Ca2+-free state Deposited 2005-02-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain I 1–137（137 aa）	Not recorded	MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1.6 M tri-Sodium Citrate dihydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 7.00 Å R-free 0.359
2W49 ISOMETRICALLY CONTRACTING INSECT ASYNCHRONOUS FLIGHT MUSCLE Deposited 2008-11-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain 2 4–144（141 aa） Fragment：RESIDUES 4-144 Chain 5 4–144（141 aa） Fragment：RESIDUES 4-144 Chain 8 4–144（141 aa） Fragment：RESIDUES 4-144 Chain Z 4–144（141 aa） Fragment：RESIDUES 4-144	Not recorded	CA CALCIUM ION × 16	ELECTRON MICROSCOPY cryo-EM buffer 20 MM MOPS BUFFER, 5 MM NAN3, AND MGCL2, ATP, CACL2, AND EGTA IN VARYING MILLIMOLAR CONCENTRATIONS；20 MM MOPS BUFFER, 5 MM NAN3, AND MGCL2, ATP, CACL2, AND EGTA IN VARYING MILLIMOLAR CONCENTRATIONS cryo-EM vitrification conditions Cryogen HELIUM；SMASH AGAINST A LIQUID HELIUM COOLED GOLD COATED COPPER MIRROR	Resolution 35.00 Å
2W4U Isometrically contracting insect asynchronous flight muscle quick frozen after a length step Deposited 2008-12-02	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 36 PDB declaration: 36-meric	Chain 2 4–144（141 aa） Fragment：RESIDUES 4-144 Chain 5 4–144（141 aa） Fragment：RESIDUES 4-144 Chain 8 4–144（141 aa） Fragment：RESIDUES 4-144 Chain Z 4–144（141 aa） Fragment：RESIDUES 4-144	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 20 MM MOPS BUFFER, 5 MM NAN3, AND MGCL2, ATP, CACL2, AND EGTA IN VARYING MILLIMOLAR CONCENTRATIONS；20 MM MOPS BUFFER, 5 MM NAN3, AND MGCL2, ATP, CACL2, AND EGTA IN VARYING MILLIMOLAR CONCENTRATIONS cryo-EM vitrification conditions Cryogen HELIUM；SMASH AGAINST A LIQUID HELIUM COOLED GOLD COATED COPPER MIRROR	Resolution 35.00 Å

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TNNI2_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–52； UniProt 131–182

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1vdi
Deposition date deposition_date	2004-03-22
Structure title title	Solution structure of actin-binding domain of troponin in Ca2+-free state
Keywords keywords	troponin, actin, tropomyosin, CONTRACTILE PROTEIN; CONTRACTILE PROTEIN
Experimental Method method	SOLUTION NMR

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	13.90 Å
Radius of gyration Rg (electron density) rg_electron	14.08 Å
Forward intensity I(0) i0	240105000.00
Molecular weight molecular_weight	122200.0 kDa
Excluded volume excluded_volume	150340 Å³
Envelope volume envelope_volume	27813 Å³
Hydration-shell volume shell_volume	13332 Å³
Envelope diameter envelope_diameter	62.5 Å
Shell Rg shell_rg	23.68 Å
Envelope Rg envelope_rg	19.45 Å
Shape Rg shape_rg	14.04 Å
Total Rg total_rg	14.54 Å
Total atoms total_atoms	15320
Residues n_residues	1040
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	58.0 Å
Rg (real space) rg_real	14.19 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	2.4010e+08
I(0) uncertainty (real space) i0_real_error	2.9310e+06
Rg (reciprocal space) rg_reciprocal	14.17 Å
I(0) (reciprocal space) i0_reciprocal	240100000.0000
Solution quality estimate total_estimate	0.7026
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	13.2 Å
Skewness Skewness skewness	0.761
Kurtosis Kurtosis kurtosis	0.338
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	110900.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.364; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.062; Smooth: 0.975

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1vdia1
Class class	j — Peptides
Fold Fold fold	j.22 — Troponin I fragments
Superfamily Superfamily superfamily	j.22.1 — Troponin I fragments
Family Family family	j.22.1.1 — Troponin I fragments

CATH v4.4 (1 domains)

Domain ID domain_id	1vdiA00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	180 —

▶

8. Citations (1)

▶

Description description	Troponin I, fast skeletal muscle
Molecular weight formula_weight	6140.0 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	15320

来源生物 organism	Gallus gallus
通用名 common_name	chicken
NCBI Class编号 ncbi_taxonomy_id	9031
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/vd/1vdi/1vdi.fit
pddf	/app/data/pr_computation/vd/1vdi/1vdi.pr.out
profile	/app/data/saxs_computation/vd/1vdi/1vdi.dat

Solution structure of actin-binding domain of troponin in Ca2+-free state

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

Troponin I, fast skeletal muscle

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

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)