SAXSdb — 3m6r

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

Peptide deformylase 1B

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	ACTINONIN × 1 ZINC ION × 5 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ACTINONIN × 1 ZINC ION × 4 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ACTINONIN × 1 ZINC ION × 5 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ACTINONIN × 1 ZINC ION × 5 water × 1	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 Author chain B； PDBConstruct 3–193； UniProt 83–273 Author chain C； PDBConstruct 3–193； UniProt 83–273 Author chain D； 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	3m6r
Deposition date deposition_date	2010-03-16
Structure title title	Crystal structure of Arabidopsis thaliana peptide deformylase 1B (AtPDF1B) G41M mutant in complex with actinonin
Keywords keywords	;peptide deformylase, 1B, PDF, N-terminal excision pathway, NME, Arabidopsis thaliana, induced-fit, Hydrolase, Metal-binding, Mitochondrion, Protein biosynthesis, Transit peptide, HYDROLASE-ANTIBIOTIC complex ;; HYDROLASE/ANTIBIOTIC
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.

3m6r__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3m6r__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3m6r__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	17.42 Å
Rg (electron density)	16.21 Å
Total Rg	17.24 Å
Atom count	1438
Residues	180
Excluded volume	25868 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3m6r__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3m6r__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3m6r__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3m6r__assembly_4__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 1B
Molecular weight formula_weight	22050.4 kDa
EC 编号 ec_number	3.5.1.88
Mutation mutation	G41M
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6178

MEIVEYPDPILRAKNKRIDIFDENLKNLVDAMFDVMYKTDMIGLSAPQVGLNVQLMVFNPAGEPGEGKEIVLVNPKIKKYSDKLVPFDEGCLSFPGIYAEVVRPQSVKIDARDITGERFSISLSRLPARIFQHEYDHLEGVLFFDRMTDQVLDSIREELEALEKKYEEKTGLPSPERVEARQKRKAGVGFGKR

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

Entity 2 Entity 2 non-polymer

Description description	ACTINONIN
Molecular weight formula_weight	385.5 kDa
Source method src_method	syn
Copy count entity_count	4

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	19

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	464

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3m6rA00
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	3m6rB00
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	3m6rC00
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	3m6rD00
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	66.640 Å
Unit-cell length b length_b	66.730 Å
Unit-cell length c length_c	189.690 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	16

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	47.150 Å
R factor r_factor	—
R_work r_work	0.2262
R_free r_free	0.2934

Crystal structure of Arabidopsis thaliana peptide deformylase 1B (AtPDF1B) G41M mutant in complex with actinonin

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

Peptide deformylase 1B

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

3m6r__assembly_3__model_1

3m6r__assembly_3__model_1 | I(q)

3m6r__assembly_3__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

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of Arabidopsis thaliana peptide deformylase 1B (AtPDF1B) G41M mutant in complex with actinonin

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

Peptide deformylase 1B

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

3m6r__assembly_3__model_1

3m6r__assembly_3__model_1 | I(q)

3m6r__assembly_3__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

CATH v4.4 (4 domains)

7. Citations (1)