SAXSdb — 1n5n

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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 monomer	Monomer	Protein 1	ZINC ION × 1 GLYCEROL × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 1 GLYCEROL × 1 water × 1	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 13–180； UniProt 1–168 Author chain B； PDBConstruct 13–180； 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	1n5n
Deposition date deposition_date	2002-11-06
Structure title title	Crystal Structure of Peptide Deformylase from Pseudomonas aeruginosa
Keywords keywords	metalloenzyme, drug design, deformylation, HYDROLASE; HYDROLASE
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.

1n5n__assembly_1__model_1

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

Download this curve (.dat)

1n5n__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1n5n__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.85 Å
Rg (electron density)	15.73 Å
Total Rg	16.70 Å
Atom count	1360
Residues	167
Excluded volume	24218 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1n5n__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1n5n__assembly_2__model_1`	monomeric （1）	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	Peptide deformylase
Molecular weight formula_weight	20866.8 kDa
EC 编号 ec_number	3.5.1.88
Mutation mutation	D84E
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	2957

MGSDKIHHHHHHMAILNILEFPDPRLRTIAKPVEVVDDAVRQLIDDMFETMYEAPGIGLAATQVNVHKRIVVMDLSEDKSEPRVFINPEFEPLTEEMDQYQEGCLSVPGFYENVDRPQKVRIKALDRDGNPFEEVAEGLLAVCIQHECDHLNGKLFVDYLSTLKRDRIRKKLEKQHRQQA

Source Source

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

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	2

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	262

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1n5na_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.167 — Peptide deformylase
Superfamily Superfamily superfamily	d.167.1 — Peptide deformylase
Family Family family	d.167.1.1 — Peptide deformylase

Domain ID domain_id	d1n5nb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.167 — Peptide deformylase
Superfamily Superfamily superfamily	d.167.1 — Peptide deformylase
Family Family family	d.167.1.1 — Peptide deformylase

CATH v4.4 (2 domains)

Domain ID domain_id	1n5nA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	45 — Peptide Deformylase
Homologous superfamily homologous superfamily	10 — Peptide deformylase

Domain ID domain_id	1n5nB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	45 — Peptide Deformylase
Homologous superfamily homologous superfamily	10 — Peptide deformylase

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Unit-cell length a length_a	68.612 Å
Unit-cell length b length_b	73.562 Å
Unit-cell length c length_c	75.995 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	8

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

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	41.870 Å
R factor r_factor	—
R_work r_work	0.1960
R_free r_free	0.2440

Crystal Structure of Peptide Deformylase from Pseudomonas aeruginosa

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

1n5n__assembly_1__model_1

1n5n__assembly_1__model_1 | I(q)

1n5n__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of Peptide Deformylase from Pseudomonas aeruginosa

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

1n5n__assembly_1__model_1

1n5n__assembly_1__model_1 | I(q)

1n5n__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)