SAXSdb — 3dmy

▼

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

Protein fdrA

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FDRA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–474； UniProt 49–522 Author chain B； PDBConstruct 1–474； UniProt 49–522

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	3dmy
Deposition date deposition_date	2008-07-01
Structure title title	Crystal Structure of a predicated acyl-CoA synthetase from E.coli
Keywords keywords	;Predicted Actyl-CoA synthetase, 10300a, NYSGRC, PSI-II, Structural Genomics, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC, Membrane, Transmembrane, unknown function ;; structural genomics, unknown function
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3dmy__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3dmy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3dmy__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	32.26 Å
Rg (electron density)	31.87 Å
Total Rg	32.25 Å
Atom count	6590
Residues	873
Excluded volume	118070 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3dmy__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Protein fdrA
Molecular weight formula_weight	51122.5 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	6952

MQQLEEALKQLAQGSGSSQALTQVRRWDSACQKLPDANLALISVAGEYAAELANQALDRNLNVMMFSDNVTLEDEIQLKTRAREKGLLVMGPDCGTSMIAGTPLAFANVMPEGNIGVIGASGTGIQELCSQIALAGEGITHAIGLGGRDLSREVGGISALTALEMLSADEKSEVLAFVSKPPAEAVRLKIVNAMKATGKPTVALFLGYTPAVARDENVWFASSLDEAARLACLLSRVTARRNAIAPVSSGFICGLYTGGTLAAEAAGLLAGHLGVEADDTHQHGMMLDADSHQIIDLGDDFYTVGRPHPMIDPTLRNQLIADLGAKPQVRVLLLDVVIGFGATADPAASLVSAWQKACAARLDNQPLYAIATVTGTERDPQCRSQQIATLEDAGIAVVSSLPEATLLAAALIHPLSPAAQQHTPSLLENVAVINIGLRSFALELQSASKPVVHYQWSPVAGGNKKLARLLERLQGHPHHH

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	362

▼

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	3dmyA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	3dmyA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	261 — Succinyl-CoA synthetase domains

Domain ID domain_id	3dmyA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	261 — Succinyl-CoA synthetase domains

Domain ID domain_id	3dmyB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	3dmyB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	261 — Succinyl-CoA synthetase domains

Domain ID domain_id	3dmyB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	261 — Succinyl-CoA synthetase domains

▶

Unit-cell length a length_a	63.574 Å
Unit-cell length b length_b	107.776 Å
Unit-cell length c length_c	153.605 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.070 Å
Low-resolution limit resolution_low	48.970 Å
R factor r_factor	0.2370
R_work r_work	0.2370
R_free r_free	0.2700

Crystal Structure of a predicated acyl-CoA synthetase from E.coli

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

Protein fdrA

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3dmy__assembly_1__model_1

3dmy__assembly_1__model_1 | I(q)

3dmy__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Crystal Structure of a predicated acyl-CoA synthetase from E.coli

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

Protein fdrA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3dmy__assembly_1__model_1

3dmy__assembly_1__model_1 | I(q)

3dmy__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)