SAXSdb — 3pn2

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

Peptide deformylase 1B, chloroplastic

Arabidopsis thaliana

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 × 6 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 12 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DEF1B_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–193； UniProt 83–273

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	3pn2
Deposition date deposition_date	2010-11-18
Structure title title	Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) (crystallized in PEG-550-MME)
Keywords keywords	peptide deformylase, 1B, PDF, N-terminal excision pathway, NME, induced-fit, 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.

3pn2__assembly_1__model_1

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

Download this curve (.dat)

3pn2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3pn2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.40 Å
Rg (electron density)	16.24 Å
Total Rg	17.20 Å
Atom count	1408
Residues	180
Excluded volume	25239 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3pn2__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3pn2__assembly_2__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 1B, chloroplastic
Molecular weight formula_weight	21976.2 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	1659

MEIVEYPDPILRAKNKRIDIFDENLKNLVDAMFDVMYKTDGIGLSAPQVGLNVQLMVFNPAGEPGEGKEIVLVNPKIKKYSDKLVPFDEGCLSFPGIYAEVVRPQSVKIDARDITGERFSISLSRLPARIFQHEYDHLEGVLFFDRMTDQVLDSIREELEALEKKYEEKTGLPSPERVEARQKRKAGVGFGKR

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	mouse-ear cress,thale-cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
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	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	251

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3pn2A00
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	56.320 Å
Unit-cell length b length_b	56.320 Å
Unit-cell length c length_c	148.440 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2052
R_work r_work	0.2026
R_free r_free	0.2575

Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) (crystallized in PEG-550-MME)

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

Peptide deformylase 1B, chloroplastic

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

3pn2__assembly_1__model_1

3pn2__assembly_1__model_1 | I(q)

3pn2__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) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of Arabidopsis thaliana petide deformylase 1B (AtPDF1B) (crystallized in PEG-550-MME)

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

Peptide deformylase 1B, chloroplastic

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

3pn2__assembly_1__model_1

3pn2__assembly_1__model_1 | I(q)

3pn2__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) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)