SAXSdb — 3edp

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

Lin2111 protein

Listeria innocua

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 7 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q92A11_LISIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–236； UniProt 1–233 Author chain B； PDBConstruct 4–236； UniProt 1–233

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	3edp
Deposition date deposition_date	2008-09-03
Structure title title	The crystal structure of the protein lin2111 (functionally unknown) from Listeria innocua Clip11262
Keywords keywords	;APC88337, lin2111, Listeria innocua Clip11262, structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics, MCSG, DNA-binding, Transcription, Transcription regulation, unknown function ;; structural genomics, 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.

3edp__assembly_1__model_1

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

Download this curve (.dat)

3edp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3edp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.79 Å
Rg (electron density)	28.56 Å
Total Rg	29.08 Å
Atom count	3636
Residues	431
Excluded volume	65836 Å³
Maximum q	0.500 Å⁻¹

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

Entity 1 Entity 1 polymer

Description description	Lin2111 protein
Molecular weight formula_weight	27452.2 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	3797

SNAMAAKKPLFEVIASKIKDSINRDEYKTGMLMPNETALQEIYSSSRTTIRRAVDLLVEEGLVVRKNGVGLYVQPKLTAQNILEMTGVMKNDTNENLKKDIKDFYIRKAGKFYAEIFGMKENELVYSIKFVQKSEHGATLDRLILPLGLYPDLQAKDFQIINIIELVNSGKYKLFELEQELQLILAGNEQIKNMHLNENDPVFKLSSVFYAENDMPIAIQYHYEDAESTKYVVDFN

Source Source

Source organism organism	Listeria innocua
NCBI taxonomy ID ncbi_taxonomy_id	1642
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	149

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3edpA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	3edpA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1410 — Chorismate lyase
Homologous superfamily homologous superfamily	10 — Chorismate lyase-like

Domain ID domain_id	3edpB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	3edpB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1410 — Chorismate lyase
Homologous superfamily homologous superfamily	10 — Chorismate lyase-like

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Unit-cell length a length_a	50.345 Å
Unit-cell length b length_b	66.620 Å
Unit-cell length c length_c	100.751 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.03 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.092 Å
Low-resolution limit resolution_low	43.367 Å
R factor r_factor	0.2021
R_work r_work	0.1999
R_free r_free	0.2424

The crystal structure of the protein lin2111 (functionally unknown) from Listeria innocua Clip11262

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

Lin2111 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

3edp__assembly_1__model_1

3edp__assembly_1__model_1 | I(q)

3edp__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

The crystal structure of the protein lin2111 (functionally unknown) from Listeria innocua Clip11262

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

Lin2111 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

3edp__assembly_1__model_1

3edp__assembly_1__model_1 | I(q)

3edp__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)