SAXSdb — 3esm

▼

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

uncharacterized protein

Nocardia farcinica

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 DIMETHYL SULFOXIDE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5Z3N8_NOCFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–144； UniProt 29–169

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	3esm
Deposition date deposition_date	2008-10-06
Structure title title	Crystal structure of an uncharacterized protein from Nocardia farcinica reveals an immunoglobulin-like fold
Keywords keywords	;STRUCTURAL GENOMICS, UNKNOWN FUNCTION, PSI-2, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC ;; 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.

3esm__assembly_1__model_1

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

Download this curve (.dat)

3esm__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3esm__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.18 Å
Rg (electron density)	19.27 Å
Total Rg	20.23 Å
Atom count	2060
Residues	272
Excluded volume	36060 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3esm__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 (4)

Entity 1 Entity 1 polymer

Description description	uncharacterized protein
Molecular weight formula_weight	16023.5 kDa
Mutation mutation	L61M, L76M
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	1164

MSLHVTADAPGAAQGGYSVVTFRVPTESETAATTAMTVTLPNVRSARTEPMPGWTARVDRNDKSEAVSVTWTADPGNPGVQPGQFQRFVVSIGPLPSAETVSFPAEQTYSDGRVVAWNQPPAANGSEPEHPAPTLTLATAPGDTEGHHHHHH

Source Source

Source organism organism	Nocardia farcinica
NCBI taxonomy ID ncbi_taxonomy_id	37329
Host organism host_organism	Escherichia coli BL21(DE3)

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	2

Entity 3 Entity 3 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	111

▼

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3esmA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2230 — Uncharacterised protein YcnI-like PF07987, DUF1775

▶

Unit-cell length a length_a	67.582 Å
Unit-cell length b length_b	67.582 Å
Unit-cell length c length_c	62.571 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 1 2
Space-group number int_tables_number	153
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2320
R_work r_work	0.2300
R_free r_free	0.2620

Crystal structure of an uncharacterized protein from Nocardia farcinica reveals an immunoglobulin-like fold

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

uncharacterized 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

3esm__assembly_1__model_1

3esm__assembly_1__model_1 | I(q)

3esm__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) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of an uncharacterized protein from Nocardia farcinica reveals an immunoglobulin-like fold

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

uncharacterized 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

3esm__assembly_1__model_1

3esm__assembly_1__model_1 | I(q)

3esm__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) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)