SAXSdb — 3c24

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

Putative oxidoreductase

Jannaschia sp.

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 4 GLYCEROL × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q28MS9_JANSC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–286； UniProt 1–285 Author chain B； PDBConstruct 2–286； UniProt 1–285

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	3c24
Deposition date deposition_date	2008-01-24
Structure title title	Crystal structure of a putative oxidoreductase (YP_511008.1) from Jannaschia sp. CCS1 at 1.62 A resolution
Keywords keywords	;YP_511008.1, A Putative Oxidoreductase, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, 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.

3c24__assembly_1__model_1

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

Download this curve (.dat)

3c24__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3c24__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.13 Å
Rg (electron density)	27.87 Å
Total Rg	28.16 Å
Atom count	4187
Residues	529
Excluded volume	74893 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3c24__assembly_1__model_1`	dimeric （2）	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 (4)

Entity 1 Entity 1 polymer

Description description	Putative oxidoreductase
Molecular weight formula_weight	31687.5 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	4908

GMVKDKNDVGPKTVAILGAGGKMGARITRKIHDSAHHLAAIEIAPEGRDRLQGMGIPLTDGDGWIDEADVVVLALPDNIIEKVAEDIVPRVRPGTIVLILDAAAPYAGVMPERADITYFIGHPCHPPLFNDETDPAARTDYHGGIAKQAIVCALMQGPEEHYAIGADICETMWSPVTRTHRVTTEQLAILEPGLSEMVAMPFVETMVHAVDECADRYGIDRQAALDFMIGHLNVEIAMWFGYSPKVPSDAALRLMEFAKDIVVKEDWREALNPAKVKQAAELIAGK

Source Source

Source organism organism	Jannaschia sp.
NCBI taxonomy ID ncbi_taxonomy_id	290400
Host organism 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	4

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	565

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3c24A01
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	3c24A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3640 — putative oxidoreductase fold
Homologous superfamily homologous superfamily	10 — Semialdehyde dehydrogenase-like, C-terminal

Domain ID domain_id	3c24B01
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	3c24B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3640 — putative oxidoreductase fold
Homologous superfamily homologous superfamily	10 — Semialdehyde dehydrogenase-like, C-terminal

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Unit-cell length a length_a	47.080 Å
Unit-cell length b length_b	80.620 Å
Unit-cell length c length_c	142.840 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	1.620 Å
Low-resolution limit resolution_low	28.456 Å
R factor r_factor	0.1630
R_work r_work	0.1610
R_free r_free	0.1950

Crystal structure of a putative oxidoreductase (YP_511008.1) from Jannaschia sp. CCS1 at 1.62 A resolution

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

Putative oxidoreductase

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

3c24__assembly_1__model_1

3c24__assembly_1__model_1 | I(q)

3c24__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of a putative oxidoreductase (YP_511008.1) from Jannaschia sp. CCS1 at 1.62 A resolution

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

Putative oxidoreductase

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

3c24__assembly_1__model_1

3c24__assembly_1__model_1 | I(q)

3c24__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)