SAXSdb — 3ejv

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

uncharacterized protein with cystatin-like fold

Novosphingobium aromaticivorans DSM 12444

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	UNKNOWN LIGAND × 3 1,2-ETHANEDIOL × 12 TRIETHYLENE GLYCOL × 3 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q2G4M1_NOVAD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–179； UniProt 1–160

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	3ejv
Deposition date deposition_date	2008-09-18
Structure title title	Crystal structure of a cystatin-like protein (saro_2766) from novosphingobium aromaticivorans dsm at 1.40 A resolution
Keywords keywords	;Cystatin-like fold, structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, unknown function ;; UNKNOWN FUNCTION
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.

3ejv__assembly_1__model_1

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

Download this curve (.dat)

3ejv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ejv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.17 Å
Rg (electron density)	22.01 Å
Total Rg	22.75 Å
Atom count	3714
Residues	456
Excluded volume	66264 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ejv__assembly_1__model_1`	trimeric （3）	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	uncharacterized protein with cystatin-like fold
Molecular weight formula_weight	20167.6 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	1536

MGSDKIHHHHHHENLYFQGMTMADETIILNVLGQYTRAHDRRDPDAMAALFAPEATIEIVDAVGGASRSISRLEGRDAIRVAVRQMMAPHGYRAWSQNVVNAPIIVIEGDHAVLDAQFMVFSILAAEVPDGGWPTGTFGAQGRIVPIEAGQYRLTLRTVADGWVISAMRIEHRLPMAFG

Source Source

Source organism organism	Novosphingobium aromaticivorans DSM 12444
NCBI taxonomy ID ncbi_taxonomy_id	279238
Host organism host_organism	Escherichia Coli

Entity 2 Entity 2 non-polymer

Description description	UNKNOWN LIGAND
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	174

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3ejva1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.4 — NTF2-like
Family Family family	d.17.4.28 — BaiE/LinA-like

CATH v4.4 (1 domains)

Domain ID domain_id	3ejvA00
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	79.540 Å
Unit-cell length b length_b	79.540 Å
Unit-cell length c length_c	79.540 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	12

Space group space_group	P 21 3
Space-group number int_tables_number	198
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	28.127 Å
R factor r_factor	0.1430
R_work r_work	0.1420
R_free r_free	0.1610

Crystal structure of a cystatin-like protein (saro_2766) from novosphingobium aromaticivorans dsm at 1.40 A resolution

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

uncharacterized protein with cystatin-like fold

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

3ejv__assembly_1__model_1

3ejv__assembly_1__model_1 | I(q)

3ejv__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

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of a cystatin-like protein (saro_2766) from novosphingobium aromaticivorans dsm at 1.40 A resolution

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

uncharacterized protein with cystatin-like fold

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

3ejv__assembly_1__model_1

3ejv__assembly_1__model_1 | I(q)

3ejv__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

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)