SAXSdb — 3ged

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

Short-chain dehydrogenase/reductase SDR

Clostridium thermocellum ATCC 27405

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	GLYCEROL × 4 THIOSULFATE × 6 SODIUM ION × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A3DFK9_CLOTH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–247； UniProt 1–247 Author chain B； PDBConstruct 1–247； UniProt 1–247

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	3ged
Deposition date deposition_date	2009-02-25
Structure title title	Fingerprint and Structural Analysis of a Apo SCOR enzyme from Clostridium thermocellum
Keywords keywords	sdr, SCOR, Rossmann Fold, Oxidoreductase; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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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.

3ged__assembly_1__model_1

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

Download this curve (.dat)

3ged__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ged__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.96 Å
Rg (electron density)	27.99 Å
Total Rg	28.78 Å
Atom count	7574
Residues	970
Excluded volume	135710 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ged__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Short-chain dehydrogenase/reductase SDR
Molecular weight formula_weight	27429.5 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	4350

MNRGVIVTGGGHGIGKQICLDFLEAGDKVCFIDIDEKRSADFAKERPNLFYFHGDVADPLTLKKFVEYAMEKLQRIDVLVNNACRGSKGILSSLLYEEFDYILSVGLKAPYELSRLCRDELIKNKGRIINIASTRAFQSEPDSEAYASAKGGIVALTHALAMSLGPDVLVNCIAPGWINVTEQQEFTQEDCAAIPAGKVGTPKDISNMVLFLCQQDFITGETIIVDGGMSKRMIYHGDWNWFYKIDK

Source Source

Source organism organism	Clostridium thermocellum ATCC 27405
NCBI taxonomy ID ncbi_taxonomy_id	203119
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	THIOSULFATE
Molecular weight formula_weight	112.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	551

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3gedA00
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	3gedB00
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

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Unit-cell length a length_a	124.287 Å
Unit-cell length b length_b	124.287 Å
Unit-cell length c length_c	162.608 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	32

Space group space_group	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	1.698 Å
Low-resolution limit resolution_low	49.684 Å
R factor r_factor	0.1800
R_work r_work	0.1790
R_free r_free	0.2080

Fingerprint and Structural Analysis of a Apo SCOR enzyme from Clostridium thermocellum

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

Short-chain dehydrogenase/reductase SDR

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

3ged__assembly_1__model_1

3ged__assembly_1__model_1 | I(q)

3ged__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Fingerprint and Structural Analysis of a Apo SCOR enzyme from Clostridium thermocellum

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

Short-chain dehydrogenase/reductase SDR

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

3ged__assembly_1__model_1

3ged__assembly_1__model_1 | I(q)

3ged__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)