SAXSdb — 2w3t

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

PEPTIDE DEFORMYLASE

ESCHERICHIA COLI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	NICKEL (II) ION × 1 CHLORIDE ION × 1 ETHANOL × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DEF_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–168； UniProt 2–169

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	2w3t
Deposition date deposition_date	2008-11-14
Structure title title	Chloro complex of the Ni-Form of E.coli deformylase
Keywords keywords	PROTEIN BIOSYNTHESIS, IRON, NICKEL, HYDROLASE, METAL-BINDING; 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.

2w3t__assembly_1__model_1

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

Download this curve (.dat)

2w3t__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2w3t__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.08 Å
Rg (electron density)	15.94 Å
Total Rg	16.96 Å
Atom count	1345
Residues	167
Excluded volume	24141 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2w3t__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	PEPTIDE DEFORMYLASE
Molecular weight formula_weight	21439.7 kDa
EC 编号 ec_number	3.5.1.31
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	1542

SVLQVLHIPDERLRKVAKPVEEVNAEIQRIVDDMFETMYAEEGIGLAATQVDIHQRIIVIDVSENRDERLVLINPELLEKSGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFMDYLSPLKQQRIRQKVEKLDRLKARAPNSSSVDKLAAALEHHHHHH

Source Source

Source organism organism	ESCHERICHIA COLI
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ETHANOL
Molecular weight formula_weight	46.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	176

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2w3ta_
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

CATH v4.4 (1 domains)

Domain ID domain_id	2w3tA00
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	82.080 Å
Unit-cell length b length_b	35.980 Å
Unit-cell length c length_c	67.590 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.43 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.690 Å
Low-resolution limit resolution_low	62.020 Å
R factor r_factor	0.2159
R_work r_work	0.2128
R_free r_free	0.2432

Chloro complex of the Ni-Form of E.coli deformylase

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

2w3t__assembly_1__model_1

2w3t__assembly_1__model_1 | I(q)

2w3t__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (2)

Chloro complex of the Ni-Form of E.coli deformylase

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

2w3t__assembly_1__model_1

2w3t__assembly_1__model_1 | I(q)

2w3t__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (2)