SAXSdb — 1dci

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

DIENOYL-COA ISOMERASE

Rattus norvegicus

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 54–327 Chain B； UniProt 54–327 Chain C； UniProt 54–327	Not recorded	SO4 SULFATE ION × 16 MG MAGNESIUM ION × 8 EDO 1,2-ETHANEDIOL × 14	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.75；pH 8.75	Resolution 1.50 Å R-free 0.205

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	ECH1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–275； UniProt 54–327 Author chain B； PDBConstruct 2–275； UniProt 54–327 Author chain C； PDBConstruct 2–275； UniProt 54–327

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	1dci
Deposition date deposition_date	1998-02-13
Structure title title	DIENOYL-COA ISOMERASE
Keywords keywords	LYASE, DIENOYL-COA ISOMERASE; LYASE
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	28.59 Å
Radius of gyration Rg (electron density) rg_electron	27.46 Å
Forward intensity I(0) i0	142031000.00
Molecular weight molecular_weight	92437.0 kDa
Excluded volume excluded_volume	115160 Å³
Envelope volume envelope_volume	135680 Å³
Hydration-shell volume shell_volume	39408 Å³
Envelope diameter envelope_diameter	86.1 Å
Shell Rg shell_rg	36.38 Å
Envelope Rg envelope_rg	27.81 Å
Shape Rg shape_rg	27.43 Å
Total Rg total_rg	28.37 Å
Total atoms total_atoms	6447
Residues n_residues	825
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	86.6 Å
Rg (real space) rg_real	28.47 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	1.4200e+08
I(0) uncertainty (real space) i0_real_error	1.7890e+06
Rg (reciprocal space) rg_reciprocal	28.52 Å
I(0) (reciprocal space) i0_reciprocal	142000000.0000
Solution quality estimate total_estimate	0.9104
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	33.1 Å
Skewness Skewness skewness	0.177
Kurtosis Kurtosis kurtosis	-0.573
Angular range angular_range	— – 0.2750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	35870000.0000
Real-space data points n_real_points	56
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.958; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.962

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	DIENOYL-COA ISOMERASE
Molecular weight formula_weight	30416.1 kDa
EC 编号 ec_number	4.2.1.17
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	7528

AYESIQVTSAQKHVLHVQLNRPEKRNAMNRAFWRELVECFQKISKDSDCRAVVVSGAGKMFTSGIDLMDMASDILQPPGDDVARIAWYLRDLISRYQKTFTVIEKCPKPVIAAIHGGCIGGGVDLISACDIRYCTQDAFFQVKEVDVGLAADVGTLQRLPKVIGNRSLVNELTFTARKMMADEALDSGLVSRVFPDKDVMLNAAFALAADISSKSPVAVQGSKINLIYSRDHSVDESLDYMATWNMSMLQTQDIIKSVQAAMEKKDSKSITFSKL

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
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	8

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	973

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7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1dcia_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.3 — Crotonase-like

Domain ID domain_id	d1dcib_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.3 — Crotonase-like

Domain ID domain_id	d1dcic_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.14 — ClpP/crotonase
Superfamily Superfamily superfamily	c.14.1 — ClpP/crotonase
Family Family family	c.14.1.3 — Crotonase-like

CATH v4.4 (6 domains)

Domain ID domain_id	1dciA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	1dciA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	12 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Lyase 2-enoyl-coa Hydratase, Chain A, domain 2

Domain ID domain_id	1dciB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	1dciB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	12 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Lyase 2-enoyl-coa Hydratase, Chain A, domain 2

Domain ID domain_id	1dciC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	226 — 2-enoyl-CoA Hydratase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — 2-enoyl-CoA Hydratase; Chain A, domain 1

Domain ID domain_id	1dciC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	12 — Lyase 2-enoyl-coa Hydratase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Lyase 2-enoyl-coa Hydratase, Chain A, domain 2

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8. Citations (1)

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Unit-cell length a length_a	131.543 Å
Unit-cell length b length_b	131.543 Å
Unit-cell length c length_c	96.731 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	18

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	—
R_work r_work	0.1760
R_free r_free	0.2050

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

DIENOYL-COA ISOMERASE

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

DIENOYL-COA ISOMERASE

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)