SAXSdb — 3g0k

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

Putative membrane protein

Novosphingobium aromaticivorans

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CALCIUM ION × 2 ACETATE ION × 4 (4S)-2-METHYL-2,4-PENTANEDIOL × 8 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q2G4A7_NOVAD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–148； UniProt 1–129

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	3g0k
Deposition date deposition_date	2009-01-28
Structure title title	Crystal structure of a protein of unknown function with a cystatin-like fold (saro_2880) from novosphingobium aromaticivorans dsm at 1.30 A resolution
Keywords keywords	;Snoal-like polyketide cyclase, structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, ca-binding protein ;; Ca-BINDING PROTEIN
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.

3g0k__assembly_1__model_1

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

Download this curve (.dat)

3g0k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3g0k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.73 Å
Rg (electron density)	18.54 Å
Total Rg	19.47 Å
Atom count	2099
Residues	248
Excluded volume	37269 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3g0k__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 (5)

Entity 1 Entity 1 polymer

Description description	Putative membrane protein
Molecular weight formula_weight	16988.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1301

MGSDKIHHHHHHENLYFQGMARTAEEQANHDLVIEMYNKVLIAMDSSAVDRYIAPGYVQHSSLAEPSVEALKGFLDRVRAESPDARQTIHRSFVDGDHVITHTHVERWPGDAGLAVVDIFRVEGGMIVEHWDVIQDVPANPVNPNSMF

Source Source

Source organism organism	Novosphingobium aromaticivorans
NCBI taxonomy ID ncbi_taxonomy_id	279238
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	181

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3g0kA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	50 —

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Unit-cell length a length_a	54.343 Å
Unit-cell length b length_b	54.343 Å
Unit-cell length c length_c	93.947 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	6

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	26.100 Å
R factor r_factor	0.1210
R_work r_work	0.1200
R_free r_free	0.1430

Crystal structure of a protein of unknown function with a cystatin-like fold (saro_2880) from novosphingobium aromaticivorans dsm at 1.30 A resolution

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

Putative membrane protein

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

3g0k__assembly_1__model_1

3g0k__assembly_1__model_1 | I(q)

3g0k__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) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of a protein of unknown function with a cystatin-like fold (saro_2880) from novosphingobium aromaticivorans dsm at 1.30 A resolution

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

Putative membrane protein

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

3g0k__assembly_1__model_1

3g0k__assembly_1__model_1 | I(q)

3g0k__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) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)