8s1x

Crystal structure of Actinonin-bound PDF1 and the computationally designed DBAct553_1 protein binder

Method: X-RAY DIFFRACTION

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

Peptide deformylase

Pseudomonas aeruginosa

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DBAct553_1 × 1 ZINC ION × 1 ACTINONIN × 1 FORMIC ACID × 8 PHOSPHATE ION × 4 POTASSIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DEF_PSEAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–168； UniProt 1–168

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	8s1x
Deposition date deposition_date	2024-02-16
Structure title title	Crystal structure of Actinonin-bound PDF1 and the computationally designed DBAct553_1 protein binder
Keywords keywords	Actinonin, de novo, computational, binder, CID, switch, deformylase, DE NOVO PROTEIN; DE NOVO 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.

8s1x__assembly_1__model_1

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

Download this curve (.dat)

8s1x__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8s1x__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.03 Å
Rg (electron density)	17.71 Å
Total Rg	18.70 Å
Atom count	3823
Residues	228
Excluded volume	34045 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8s1x__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 (8)

Entity 1 Entity 1 polymer

Description description	Peptide deformylase
Molecular weight formula_weight	19391.2 kDa
EC 编号 ec_number	3.5.1.88
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	3921

MAILNILEFPDPRLRTIAKPVEVVDDAVRQLIDDMFETMYEAPGIGLAATQVNVHKRIVVMDLSEDKSEPRVFINPEFEPLTEDMDQYQEGCLSVPGFYENVDRPQKVRIKALDRDGNPFEEVAEGLLAVCIQHECDHLNGKLFVDYLSTLKRDRIRKKLEKQHRQQA

Source Source

Source organism organism	Pseudomonas aeruginosa
NCBI taxonomy ID ncbi_taxonomy_id	287
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DBAct553_1
Molecular weight formula_weight	8152.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DYIRELRAALILLALKKQHAEDPDAQRVADELMKKLFDAAHRNDKDKVKKVVEEAKKVVSTYGSHHHHHH

Source Source

Source organism organism	synthetic construct
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ACTINONIN
Molecular weight formula_weight	385.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 6 Entity 6 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	76

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Unit-cell length a length_a	49.440 Å
Unit-cell length b length_b	75.010 Å
Unit-cell length c length_c	83.160 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	1.880 Å
Low-resolution limit resolution_low	55.700 Å
R factor r_factor	0.1846
R_work r_work	0.1837
R_free r_free	0.2027

Crystal structure of Actinonin-bound PDF1 and the computationally designed DBAct553_1 protein binder

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

Peptide deformylase

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

8s1x__assembly_1__model_1

8s1x__assembly_1__model_1 | I(q)

8s1x__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)

Crystal structure of Actinonin-bound PDF1 and the computationally designed DBAct553_1 protein binder

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

Peptide deformylase

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

8s1x__assembly_1__model_1

8s1x__assembly_1__model_1 | I(q)

8s1x__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)