SAXSdb — 1dcf

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

ETR1 PROTEIN

Arabidopsis thaliana

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 603–738	Fragment：RECEIVER DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；Li2SO4, HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP	Resolution 2.50 Å R-free 0.271

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 1DCF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4PL9 Structure of the catalytic domain of ETR1 from Arabidopsis thaliana Deposited 2014-05-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 407–589（183 aa） Fragment：residue 407-589	Not recorded	CD CADMIUM ION × 11 CL CHLORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；50 mM Cadmimum sulfate, 0.1 M HEPES pH 7.5, 1.0M Sodium acetate	Resolution 1.90 Å R-free 0.182

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ETR1_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–136； UniProt 603–738

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	1dcf
Deposition date deposition_date	1999-11-04
Structure title title	CRYSTAL STRUCTURE OF THE RECEIVER DOMAIN OF THE ETHYLENE RECEPTOR OF ARABIDOPSIS THALIANA
Keywords keywords	BETA-ALPHA FIVE SANDWICH, TRANSFERASE; TRANSFERASE
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	15.70 Å
Radius of gyration Rg (electron density) rg_electron	14.20 Å
Forward intensity I(0) i0	4414740.00
Molecular weight molecular_weight	14622.0 kDa
Excluded volume excluded_volume	18250 Å³
Envelope volume envelope_volume	20832 Å³
Hydration-shell volume shell_volume	12475 Å³
Envelope diameter envelope_diameter	51.5 Å
Shell Rg shell_rg	20.11 Å
Envelope Rg envelope_rg	14.72 Å
Shape Rg shape_rg	14.21 Å
Total Rg total_rg	15.41 Å
Total atoms total_atoms	1020
Residues n_residues	133
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	52.1 Å
Rg (real space) rg_real	15.60 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	4.4150e+06
I(0) uncertainty (real space) i0_real_error	5.3180e+04
Rg (reciprocal space) rg_reciprocal	15.61 Å
I(0) (reciprocal space) i0_reciprocal	4415000.0000
Solution quality estimate total_estimate	0.7241
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.1 Å
Skewness Skewness skewness	0.129
Kurtosis Kurtosis kurtosis	-0.278
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	726600.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.776; Stabil: 1.000; Sysdev: 0.368; Positv: 1.000; Valcen: 1.000; Smooth: 0.977

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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1dcfa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.1 — CheY-like
Family Family family	c.23.1.2 — Receiver domain of the ethylene receptor

CATH v4.4 (1 domains)

Domain ID domain_id	1dcfA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	2300 — Response regulator

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8. Citations (1)

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Unit-cell length a length_a	47.920 Å
Unit-cell length b length_b	47.920 Å
Unit-cell length c length_c	111.790 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	500.000 Å
R factor r_factor	0.2270
R_work r_work	0.2220
R_free r_free	0.2709

Description description	ETR1 PROTEIN
Molecular weight formula_weight	15304.9 kDa
EC 编号 ec_number	2.7.3.-
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1061

CRYSTAL STRUCTURE OF THE RECEIVER DOMAIN OF THE ETHYLENE RECEPTOR OF ARABIDOPSIS THALIANA

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

ETR1 PROTEIN

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

来源 Source

Entity 2 Entity 2 water

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)

来源生物 organism	Arabidopsis thaliana
通用名 common_name	thale cress
NCBI Class编号 ncbi_taxonomy_id	3702
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	41

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