SAXSdb — 1zy0

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

Peptide deformylase, mitochondrial

Arabidopsis thaliana

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DEFM_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–190； UniProt 69–257 Author chain B； PDBConstruct 2–190； UniProt 69–257

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	1zy0
Deposition date deposition_date	2005-06-09
Structure title title	X-ray structure of peptide deformylase from Arabidopsis thaliana (AtPDF1A); crystals grown in PEG-6000
Keywords keywords	peptide deformylase; PDF1A; eukaryote; higher plant; Arabidopsis thaliana; zinc ion, 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.

1zy0__assembly_1__model_1

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

Download this curve (.dat)

1zy0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1zy0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.07 Å
Rg (electron density)	23.43 Å
Total Rg	24.17 Å
Atom count	2944
Residues	382
Excluded volume	52370 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1zy0__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	Peptide deformylase, mitochondrial
Molecular weight formula_weight	22310.7 kDa
EC 编号 ec_number	3.5.1.88
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	3035

MDLPEIVASGDPVLHEKAREVDPGEIGSERIQKIIDDMIKVMRLAPGVGLAAPQIGVPLRIIVLEDTKEYISYAPKEEILAQERRHFDLMVMVNPVLKERSNKKALFFEGCLSVDGFRAAVERYLEVVVTGYDRQGKRIEVNASGWQARILQHECDHLDGNLYVDKMVPRTFRTVDNLDLPLAEGCPKLGSHHHHHH

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	thale cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
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	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	91

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1zy0a1
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.167.1.0 — automated matches

Domain ID domain_id	d1zy0a2
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	d1zy0b1
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.167.1.0 — automated matches

Domain ID domain_id	d1zy0b2
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	1zy0A00
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	1zy0B00
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	51.500 Å
Unit-cell length b length_b	76.800 Å
Unit-cell length c length_c	109.300 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	2.900 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.2430
R_free r_free	0.2830

X-ray structure of peptide deformylase from Arabidopsis thaliana (AtPDF1A); crystals grown in PEG-6000

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

Peptide deformylase, mitochondrial

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

1zy0__assembly_1__model_1

1zy0__assembly_1__model_1 | I(q)

1zy0__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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)

X-ray structure of peptide deformylase from Arabidopsis thaliana (AtPDF1A); crystals grown in PEG-6000

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

Peptide deformylase, mitochondrial

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

1zy0__assembly_1__model_1

1zy0__assembly_1__model_1 | I(q)

1zy0__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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (1)