SAXSdb — 3lnl

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

UPF0135 protein SA1388

Staphylococcus aureus subsp. aureus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	ZINC ION × 12 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y1388_STAAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–370； UniProt 1–366 Author chain B； PDBConstruct 5–370； UniProt 1–366

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	3lnl
Deposition date deposition_date	2010-02-02
Structure title title	Crystal structure of Staphylococcus aureus protein SA1388
Keywords keywords	PROTEIN SA1388, SELENOMETHIONINE SAD, 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.

3lnl__assembly_1__model_1

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

Download this curve (.dat)

3lnl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3lnl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.62 Å
Rg (electron density)	39.68 Å
Total Rg	40.20 Å
Atom count	15537
Residues	1968
Excluded volume	278590 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3lnl__assembly_1__model_1`	hexameric （6）	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	UPF0135 protein SA1388
Molecular weight formula_weight	41606.2 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	5914

AMDPMKIADLMTLLDHHVPFSTAESWDNVGLLIGDEDVEVTGVLTALDCTLEVVNEAIEKGYNTIISHHPLIFKGVTSLKANGYGLIIRKLIQHDINLIAMHTNLDVNPHGVNMMLAKVMGLKNISIINNQQDVYYKVQTYIPKDNVGPFKDKLSENGLAQEGNYEYCFFESEGRGQFKPVGEANPTIGQIDKIEDVDEVKIEFMIDAYQKSRAEQLIKQYHPYETPVFDFIEIKQTSLYGLGVMAEVDNQMTLEDFAADIKSKLNIPSVRFVGESNQKIKRIAIIGGSGIGYEYQAVQQGADVFVTGDIKHHDALDAKIHGVNLIDINHYSEYVMKEGLKTLLMNWFNIEKINIDVEASTINTDPFQYI

Source Source

Source organism organism	Staphylococcus aureus subsp. aureus
NCBI taxonomy ID ncbi_taxonomy_id	158879
Host organism host_organism	ESCHERICHIA COLI BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	282.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	692

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3lnla1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.135 — NIF3 (NGG1p interacting factor 3)-like
Superfamily Superfamily superfamily	c.135.1 — NIF3 (NGG1p interacting factor 3)-like
Family Family family	c.135.1.0 — automated matches

Domain ID domain_id	d3lnla2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3lnlb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.135 — NIF3 (NGG1p interacting factor 3)-like
Superfamily Superfamily superfamily	c.135.1 — NIF3 (NGG1p interacting factor 3)-like
Family Family family	c.135.1.0 — automated matches

Domain ID domain_id	d3lnlb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	3lnlA02
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily	300 —

Domain ID domain_id	3lnlB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

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Unit-cell length a length_a	132.547 Å
Unit-cell length b length_b	132.547 Å
Unit-cell length c length_c	125.670 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	18

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	33.140 Å
R factor r_factor	0.1512
R_work r_work	0.1491
R_free r_free	0.1905

Crystal structure of Staphylococcus aureus protein SA1388

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

UPF0135 protein SA1388

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

3lnl__assembly_1__model_1

3lnl__assembly_1__model_1 | I(q)

3lnl__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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of Staphylococcus aureus protein SA1388

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

UPF0135 protein SA1388

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

3lnl__assembly_1__model_1

3lnl__assembly_1__model_1 | I(q)

3lnl__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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)